Fracture
by Fitzroy
Summary: Aftermath of John's run-in with the Sakari. Spoilers for entire series up to Remnants with hints of Brain Storm.


Disclaimer: Wish I owned 'em. If I did, I'd be begging all of you brilliant writers for your ideas, they wouldn't have cancelled the show and we'd see John shirtless more often...Actually have we ever??

Author's Note: Just a few quick, heartfelt thank yous to some amazing women that I couldn't have done this without. Erin87, thank you for making me feel welcome while I reviewed your amazing works and a lot less like a stalker because I hadn't posted any of my own. Frisco, all the thank yous I could ever utter will never be enough to express how much I appreciate the permission to use Merkat from Trial by Fire. I didn't use him but I couldn't let your graciousness go unnoticed. Gator101, thank you for writing an amazing ficlet that helped bring this headache of a story to life. To Bailadora for betaing this...this...cause of many sleepless nights, headaches and tears. You may not know who any of these people are that you were reading about but that makes you all the more precious to me. Tons of hugs, love, sugar and carrots to you and Dancer. Lastly and most important of all, this is dedicated to Azure Lupis. You wouldn't let me give up on Fracture when all I wanted to do was rip my hair out. You've been an amazing source of friendship, inspiration and laughter, and all because you asked me about my pseudonym. I know for a fact there is no way I could have done this without you giving me encouragement and all those Sheppard cookies and the chocoraisimeal sandwich cookies...by the way my stash is gettin' low, but this time could you make them Henry red velvet cupcakes...you know why ;) Okay...on with the show...

***

"So Kanaan, what'd ya think of the movie?" John asks, turning to see the bewildered expression on the Athosian's face.

"It was…interesting?"

Teyla suddenly steps forward before John is able to ask another question. "Yes… Interesting. It is time to say goodnight I think. Amelia has been gracious enough to watch Torren but I do not want to take advantage of her generosity."

"We were gonna watch Alien vs. Predator Requiem, that one's much better than the first. I'm sure Banks wouldn't mind watching the little guy for a few more hours."

"Thank you for the invitation, Colonel. I think we had better retire for the evening, it has been a long day." Teyla smiles as sincerely as she can while she and Kanaan leave the room.

"Okay, so who else is up for AVPR?" John asks, turning to the people remaining in the room.

"I think I'd better turn in. I've got rounds in the morning and like Teyla said, it's been a long day." Jennifer stands and stretches while Rodney stands with her.

"I'll walk you as far as the transporter; there might still be something in the mess suitable for a midnight snack. Night all."

"It's not even ten o'clock McKay." Trying to hide his exasperation, John looks at his watch and then at the astrophysicist.

"Yeah, well like Jennifer said, it's been a long day with the Sakari and everything."

John waves him away and turns to Ronon "What about you big guy? You up for another movie?"

The younger man wordlessly looks in the direction Teyla and Kanaan just walked and then back at John.

John shakes his head sadly "Go, before she makes it to her quarters and you need to make up yet another excuse as to why you're there," he says dejected. Ronon smiles and strides away.

Looking around the room John realizes the only person left is the new expedition leader, Richard Woolsey.

"I've got reports to go over before I turn in; I should really call it a night," Woolsey smiles awkwardly, backing out of the room.

John sighs looking around the now empty room, "I didn't want to watch it either." Stepping out into the hallway and making sure the motion sensitive lights turn off; John's eyes wander around, taking in all the details of the room. One in particular catches his eye, the DVD case for When Harry Met Sally. A shadow of a smile crosses the Colonel's face remembering that the movie was one of former expedition leader Elizabeth Weir's favorites. "Night 'Lizabeth," he murmurs softly to the dark room before sauntering to his quarters.

Once there, sleep eludes John as it usually does, but he has discovered a sure fire way to cure the insomnia. Picking up his well worn copy of War and Peace, John settles onto his bed and begins to read, letting the words lull him to sleep.

As always the nightmare begins benignly enough with memories of past missions, when suddenly the image of Acastus Kolya comes from out of nowhere and John realizes his surroundings have changed; he is kneeling in front of his enemy with ropes around his wrists, arms spread eagle.

"_Last chance Johnny boy," Kolya says in a cold tone, raising the machete high over his head._

_John looks straight into the older man's eyes, not knowing how to stop him._

"_Didn't think so." Kolya swings the machete downward toward John's left wrist with all his might._

_John opens his mouth to scream but no sound comes out. He looks down in disgusted wonder to see his left hand bandaged and bound._

Suddenly John jerks awake, hearing his name being called over the radio.

"_Colonel Sheppard come in, Colonel Sheppard? Colonel, are you there?"_ Woolsey's voice begins to edge with concern the longer the page goes unanswered.

"Go ahead," John sits up, putting the earpiece in with his right hand while scrubbing his left over his face to wipe the sweat off.

"_You missed the morning briefing and no one had seen you since last night. Are you all right?"_ Woolsey asks while John looks down at his left hand, flexing it, swearing he feels a phantom pain moving up his arm.

"Sorry about that, I forgot to set my alarm and overslept," John apologizes, checking his watch and seeing the alarm was not set.

"_Well you didn't miss much, but you do need to check in with Dr. McKay. He needs your help with some tests he needs to run on the Chair. He's expecting you."_

"Will do, Sheppard out," John sighs, mentally preparing himself for a day in the Chair Room with Rodney.

* * *

"Well, look who decided to grace us with his presence. I need to run some diagnostics on the Chair since it's been a year since we've used it. Can you believe that?" Rodney comments sarcastically as John walks into the Chair room, stopping short when he sees the Chair.

"Has it been that long? Wow times flies," John says softly, remembering vividly the last time he used the Chair. He had been trying to land the City on this new planet Atlantis now called home.

"Over a year actually," Radek Zelenka murmurs softly near John's shoulder, looking up from his computer screen, pushing his glasses up the bridge of his nose.

"Have a seat, this shouldn't take long." Rodney pats the Chair's arm, motioning for John to sit.

"Where've I heard that before," John snipes back sitting down. The Chair instantly responds to his presence, lighting up and reclining. When it does, John is suddenly swamped with memories of the first time he ever sat in an Ancient Chair.

"_The specific gene is very rare, but on the whole they look very much like we do. In fact they were first, we're the second evolution of this form, the Ancients having explored the galaxy for millions of years before," Dr. Carson Beckett explains to John who is walking around the Chair, poking at it here and there._

_Then John steps up to stand in front of the Chair and turns to sit down. "Major, please don't…"_

"_Come on, what are the odds of me having the same genes as these guys?" John asks sitting down. The Chair immediately lights up and reclines, John looks over at Beckett with a panicked look on his face._

"_Quite slim actually," Carson looks around. "Dr, Weir," he shouts. Not seeing the person he is looking for, glances back at John. "Don't move." Carson rushes off to another part of the ice cave to look for the expedition's leader, Dr. Elizabeth Weir._

_As Carson, Elizabeth and Rodney rush back into the Chair room they are followed by Dr. Daniel Jackson and Brigadier General Jack O'Neill of the original Stargate team._

"_Who is this?" Elizabeth gestures to John._

_Jack steps up on the platform to look down at John who is still reclining in the Chair. "I said don't touch anything."_

"_I…I just sat down." _

_Rodney steps forward, wanting to know just how much John is capable of. "Major, think about where we are in the solar system." Suddenly a holographic 3-D image of a star system appears above everyone._

_John looks up confused and bewildered "Did I do that?"_

"Whoa, what was that?" Rodney's computer beeps, getting his attention, breaking through John's memories and bringing him back to the present.

"What was what?"

"That was my question." Rodney looks at John like he is a child, granted a child with a 9mm strapped to his leg.

"I'm just sittin' here, just like you told me to," John remarks, speaking the last six words slowly to goad the scientist.

"Then what is going on?" Rodney turns to Zelenka, who is studying his computer intently.

"I have no explanation. The system was going along fine and then it just…spiked. Could it have something to do with whatever Colonel Sheppard was thinking about?"

Rodney looks at Radek like he said something in his native Czechoslovakian tongue.

While the scientists glare at each other silently, Ronon saunters in and jerks his head in greeting to Sheppard. "Hey, wanna spar? Teyla wimped out on me."

"Sure," John jumps out of the Chair and looks over at Rodney. "Let me know how the tests come out."

"Really?" Rodney, thinking the Colonel is interested, perks up.

"No," John says in passing and Rodney huffs out a breath, realizing that John got the better of him. John turns his attention to his Satedan friend walking out of the Chair room. "So why'd Teyla bail on you?"

"Oh don't worry we'll get that power spike all figured out, don't you worry," Rodney says, hearing something about Teyla's son Torren still being colicky coming from Ronon.

"I was a colicky baby, my mom just let me cry," he says awkwardly as Radek looks over his computer at the younger man. I'm no worse for it."

With that said Radek walks away mumbling something in his native language and shaking his head. "Well I'm not," Rodney snipes rushing to catch up to Radek.

* * *

"So I was thinking," John pants out while he and Ronon dance around each other, each holding a wooden bantos sword. "We have some leave coming. Got any ideas on how you want to spend it?"

"Lemme think about it and I'll get back to ya," Ronon huffs out, lunging forward and attacking John with a series of blows.

"Give some thought to camping on the mainland," John manages to deflect some of the blows but gets nicked in the back, jumping away in pain. "There are some great looking beaches that look like they'd have surfing potential." John lashes back with a barrage that the Satedan is able to deflect with ease.

Ronon lunges at John without striking out, trying to keep the older man off balance. "Has Keller cleared you for duty yet?"

"There was never anything medically wrong with me to begin with. It was all in my head," John says irritably thinking about what the Sakari A.I. had put him through. "What they said I put myself through," John mutters under his breath.

"Sheppard," Ronon shouts sharply, but it's too late. John's concentration falters away from the sparring, allowing Ronon an easy hit. Unfortunately for John it was to the side of his head, a shot he should have seen coming had he been paying attention. "Woolsey's not gonna like this," Ronon comments to the unconscious form of his team leader at his feet. "Neither is Keller. She's always telling me to take it easier on you," Ronon lifts John up in a fireman's carry to take him to the Infirmary, chuckling sadly.

"_How'm I doin'?" John asks, looking across the infirmary to where Carson and Elizabeth are standing._

_Elizabeth walks over to him warily, trying to figure out what to say._

"_Anything that has you speechless has me concerned." _

_Elizabeth does her best to smile sincerely, but from the look on John's face she can tell it's not coming out right. "You're gonna be fine."_

"_Wow, that's dead man talk."_

_The expedition leader looks away from John. "No it isn't."_

_John turns up his right arm to show Elizabeth the wound Ellia had inflicted. "Have you seen this?"_

"_Beckett is gonna figure this one out."_

"_I think I already have. You know who I'm starting to feel like?" John looks at Elizabeth. "Ford."_

"_Now what happened to you is completely different."_

"_I know, I know. Still I can feel it. I mean, I can feel it changing me inside…like he did."_

_Elizabeth looks back at John, shifting uneasily. "We're gonna beat this."_

_John looks up at her incredulously, "We're gonna beat this? Beckett'll figure this out? You're gonna be fine? You really suck at this whole bedside manner thing."_

"_I know, I'm sorry," Elizabeth looks away embarrassed._

"_But I appreciate the effort."_

Suddenly the images change in John's mind. It's as if he's watching a playback of himself while slowly mutating into an Iratus bug/Wraith hybrid. He sees himself sparring with Teyla, backing her into a wall and forcibly kissing her. Warning Elizabeth to authorize more security for outside his door while she looks helplessly at his changing appearance. Then the nightmare changes again and suddenly John is seeing everything through his mutating yellow eyes. He sees Elizabeth standing in his dark quarters, speaking to him in that soft voice.

"_The nest was too well protected. We were unable to retrieve the eggs. They tried their best…"_

"_Best?" is all John can get out._

"_The bugs attacked…"_

_John interrupts Elizabeth, "Try again."_

"_Can't do that," Elizabeth manages, looking John in the eye._

"_Why?"_

"_John…"_

"_No."_

"_I understand…"_

_John interrupts again, this time saying something Elizabeth isn't prepared to hear. "If you won't, then kill me now."_

"_John…"_

"_It's better for the both of us."_

_Elizabeth shakes her head in defiance. "I can't do that."_

_John takes a menacing step forward. "Then try again."_

_Elizabeth shakes her head imperceptibly, holding eye contact with her Military Commander, but that's all it takes for John to realize her decision. He lunges forward, grabbing Elizabeth around the throat and squeezing, feeling her pulse jump madly under his hand._

"_We lost Walker and Stevens," she gasps out, then struggling to take in a breath. "I won't send another team," she gasps again. "I won't risk more lives."_

_Upon hearing this John's hand tightens reflexively in anger and frustration and then, just as suddenly as he grabbed Elizabeth, John lets her go, turning away while she hits the floor totally unprepared._

Suddenly John comes awake with a start, sitting up, breathing heavily and looking around, trying to get his breath.

"Whoa what was that?" Rodney asks suddenly, sitting in his lab, hearing his laptop beep as it did earlier. "What is going on around here?" Another power spike has been caught.

Slowly John realizes he's in the Infirmary. Looking to his right he sees Ronon standing back, watching over him. "What happened?"

"We were sparring. You lost concentration and I cracked you a good one, sorry about that. I brought you here to make sure I didn't do any real damage," Ronon replies in his characteristic low voice, pushing off the wall and walking to Sheppard's bedside.

"Which you managed not to do," Jennifer says, entering the room, carrying a scan of John's head. "You're lucky, just a little bump, no concussion. Please be more careful," she stresses, looking at John. "By the way, Dr. Kwiatkowski is expecting you after lunch, Colonel."

"Thanks Doc. Come on big guy, I'm starved." John leads Ronon out of the Infirmary to the mess hall, tapping his comm as he goes. "Hey McKay, you had lunch yet?"

"_Since I haven't figured out where the power spikes are coming from or why for that matter, the answer to your question would be no, Colonel. I haven't been away from my lab, since you left the Chair Room."_

"Did you say spikes? There was only the one this morning."

"_There was another one about a minute ago. Didn't you get the message I sent you?"_

"I haven't been near my office since yesterday Rodney. I've spent the morning passed out in the Infirmary."

"_What the hell have you been doing there?" _Rodney asks gruffly, trying to cover his worry.

"Did you not hear me? I said I was unconscious. Ronon and I were sparring and he got a lucky shot. I'm fine by the way, thanks for asking."

"_As much as I'd like to hear the story about the two of you beating each other with sticks like a couple of lower Paleolithic cavemen, us evolved Homo Sapiens have important work that needs to be done."_

"Come on McKay, take a break. Meet us in the mess hall; I'll let you have my Jell-O."

"_It _is_ blue Jell-O today and that is my favorite." _Rodney mumbles to himself as John smiles at Ronon._ "Okay, let me wrap a few things up and I'll meet you and Ronon there."_

"See, now was that so hard? Sheppard out."

Forty-five minutes later, Rodney is setting his food-laden tray in front of Sheppard and his computer tablet to his right.

"Glad you could make it, appreciate you workin' lunch into your schedule," John says sarcastically while Rodney glares across the table at him.

"I do remember telling you that I was particularly busy right now and you seduced me with the thought of Jell-O, specifically blue Jell-O. When I went through the line all they had left were lemon bars…_lemon_," Rodney snipes back, feeling betrayed.

John reaches over to the chair next to him. "Keep your shirt on McKay, I grabbed extra for you."

Ronon nods at Rodney's tablet. "Why'd you bring that with you?"

"Do neither of you remember me saying that I was trying to figure out what has been causing the power spikes that have happened. I've been running tests all morning. By the way, we need to go back to the Chair Room and finish running the diagnostic tests," Rodney manages to get out while inhaling his food.

"I thought we got that all done this morning," John says innocently enough for Rodney not to buy it.

"Nice try Colonel. We had to suspend the tests when you got out of the Chair to go play Don Quixote."

John exchanges a questioning look with Ronon. "I thought the tests were done. By the way, are you implying that sparring is a lost cause for me, Jet Li?"

"No, merely pointing out that any hope of ever besting Ronon is a lost cause. One, I might add, I've already conceded."

"Who the hell is Don Quixote?" Ronon asks, yet again becoming totally lost in the conversation.

"Don Quixote was a fictional character who liked to fight windmills. He was nuts," Rodney supplies while John shakes his head.

"It doesn't matter who he was. Rodney's basically saying I'm nuts for sparring with you."

"Well I coulda' told you that." Ronon stands and leaves the table, smirking.

Rodney's conceited smirk is enough of an incentive for the Colonel to get up and leave the astrophysicist alone with his lunch.

"Hey! The Chair Room," Rodney shouts at John before he is able to get three steps away from the table.

John turns and opens his mouth to compare Don Quixote's sidekick Sancho Panza to McKay, but he is cut off by his radio.

"_Colonel Sheppard, the Daedalus has arrived in orbit. I thought you might want to welcome Colonel Caldwell,"_ Woolsey's voice comes through the comm.

"On my way," John taps his comm closed. "Looks like I've gotta go. I'll see you later."

"Yes, you will," Rodney says loudly, with a certainty that has John looking over his shoulder.

While John climbs the stairs from the Gate Room up to the Control Room he can see that Colonel Caldwell is already in Woolsey's office.

"Don't misunderstand me Mr. Woolsey, I have great respect for Colonel Sheppard, but don't you find it a little more than odd that he doesn't want to leave Atlantis for even a few weeks? After everything you've all been through these last few months, I know I'd be chomping at the bit to get out of this City for a while," Caldwell admits and John realizes the Colonel is talking about him.

"It's not that I don't want to leave the City, Colonel. It's being cooped up on the Daedalus for three weeks. The last time I spent that much time on your ship the Wraith uploaded a virus and tried to kill us and all I got was nice sunburn for my troubles, so please forgive me if I'm a little reluctant to make a repeat performance," John says seriously, with a little hint of humor. "Besides there's no real reason for me to go home, I just talked to my brother the other day and everything is good with him so I figure I'll just stick close to the City while the others go."

"Well, we're not leaving for a few more days so you still have time to change your mind." Caldwell stands as does Woolsey. "I'd better head back.

"I'll walk with you." Woolsey moves from behind his desk following Caldwell, stopping beside John. "Don't forget your appointment Colonel."

John winces visibly, hoping Woolsey won't say more in front of Caldwell. This is all John wants; a commanding officer to know he has to see a shrink. Especially _this_ commanding officer.

Woolsey sees John visibly tensing "I had to see her as well Colonel. It's the only way Dr. Keller will clear you for not only active duty but _any_ kind of Gate travel. It's painless, trust me," the expedition leader murmurs quietly, trying not to attract attention.

"You see her of your own free will and I'm fine. I don't see what going to see a head doctor is gonna to do for me," John protests looking beyond Woolsey to see Caldwell standing a respective distance away. "I've never had to go after any of our other missions before."

"This was a little different; I think Dr. Keller is a little worried about the mental ramifications of what the Sakari put us _all_ through."

"Then why doesn't McKay have to go?" John questions, not caring if he sounds like a little kid; he doesn't like being singled out.

"Because the Sakari didn't manifest the torturous subterfuge for Dr. McKay-or myself for that matter-that they felt was necessary to deceive you with." Woolsey takes a deep breath. "If you like, I can strongly suggest to Dr. Keller that you are more than fit for active duty, that way you only need to see Dr. Kwiatkowski once."

"I appreciate the thought, but we both know Keller will clear me when she's good and ready," John states matter-of-factly, while his comm beeps. "This is Sheppard go ahead."

"_Well I'm done with the lunch you begged me to get and then abandoned me to, so I figure you owe me. Back to the Chair?"_ Rodney's voice comes over the comm loud and clear while Woolsey and Caldwell both look at John with a raised eyebrow.

"_Now_ who's Don Quixote? Sorry McKay, I forgot I have an appointment that I have to keep and no, I can't get out of it," John answers Rodney's unasked question. "Not unless you want a new team leader," he says quietly, not wanting Caldwell to hear-or anyone else for that matter.

"_Ah yes _that_ appointment."_ Rodney's understanding was a balm and welcome feeling for Sheppard, but with Rodney it never lasts long. _"Well, don't take too long, we need to get these tests done."_

Woolsey steps forward, tapping his comm to activate it. "Colonel Sheppard will take as long as he needs Dr. McKay. Is that understood?"

"_Perfectly,"_ Rodney clips out as Radek tries to conceal a smirk behind his back. "Not a word Zelenka. Not one word."

"Thanks," John says quietly, glancing at Caldwell still standing to attention, waiting for Woolsey. "I'll let you know about the tests when McKay gets them done," John says in a louder voice so Caldwell can hear them.

"See that he does, Colonel," Woolsey replies, putting a hand to John's back in a reassuring manner.

While John walks through the Control Room and down the back stairs as to avoid as many personnel as possible, Woolsey turns to Caldwell.

"Shall we Colonel? I am so sorry for that interruption; sometimes Dr. McKay…"

Caldwell puts up a hand to stop Woolsey's rambling. "Mr. Woolsey, please don't take this the wrong way but I've seen a lot of things that I never thought I would in two galaxies, and the one thing I'd know like the back of my hand is a solider tortured by something he's seen or been through. Since I've seen the kind of man John Sheppard is, I will assume that you will do whatever it takes to make sure he gets the help he needs and to ensure the safety of this City."

"Of course Colonel; I would do no less for either."

"Then I have no cause for worry. If I'm not mistaken there is a video of a certain Yorkie in the mail delivery that I think you'll want to see," Caldwell says seeing relief and then delight flit across Woolsey's face.

"Dr. Kwiatkowski, this is Colonel Sheppard, please respond," John taps his comm to communicate with the new doctor.

"_Go ahead Colonel,"_ a young woman's voice comes over the link, surprising Sheppard.

"Umm, I know we have an appointment and I should have looked into this beforehand, but I just realized that I have no idea where your office is in the City. I went to Dr. Heightmeyer's old office and there's no one here." John looks around uncomfortably, remembering the pretty strawberry blonde doctor who had jumped to her death the year before.

"_I tell you what. It's a beautiful day. How about we meet on the balcony off the Control Room?"_

John shifts in his boots uncomfortably, running a hand over the back of his neck. "I…I was hoping that we could have a little more privacy, like say…your office."

"_If you wish, Colonel. I was just thinking that a more relaxed setting would make you more comfortable and I've heard that you and Dr. Weir spent a lot of time there."_

"Oh she's good," John mutters absently while thoughts of Elizabeth flit through his mind. "How about we compromise? I'll meet you on the South Pier. It'll give us a great view of the City and the water and it's relatively quiet this time of day."

"_That sounds like a great compromise Colonel, I'll meet you there."_

While John walks to the southern side of the City, he watches for any sign that he might be needed so as to draw out getting to the pier before Dr. Kwiatkowski. "I don't want her to think I'm really gung-ho about this," he muses aloud, not noticing the curious looks from expedition members.

"_Just one more thing to fail at, huh Johnny boy?" _Kolya's voice suddenly resounds through John's head, causing him to falter in surprise and draw his 9mm sidearm.

"Colonel Sheppard? Are you all right?" a young auburn haired, hazel-eyed beauty asks as John stops and scans the area for Kolya.

"I'm fine, sorry if I scared you." John apologizes, securing his sidearm.

"No need to apologize. Might I suggest we continue our walk to the pier together?" the young woman suggests and realization dawns on John.

"Dr. Kwiatkowski?"

"Riley, please. We're trying to be as informal as possible. This is an evaluation, not a full-on session. We'll only get to those if you deem it necessary," Riley says quite plainly as John looks at her in surprise.

"I would think that would be something that was determined by you."

"I've read your file, Colonel, and in my professional opinion you are as mentally sound as any of us can be living out here in another galaxy. Dr. Keller and Mr. Woolsey are simply concerned for your well-being. What you were subjected to on the mainland was torture, make no mistake about that."

"So they want to make sure I don't suddenly flip out and start shooting my team or any civilians." John surmises while Riley smiles understandingly at him.

"From what I could gather, they are more concerned about you hurting yourself above hurting your team or anyone in the City."

John stops walking, turning to look at the woman next to him with surprise and disbelief in his green-hazel eyes. "They think I'm suicidal!"

"In your report of what happened on the mainland you stated that the A.I. told you it was only feeding off your darkest fears. I don't believe Dr. Keller and Mr. Woolsey _currently_ think you are suicidal, when they consulted with me they expressed concern that you might have unresolved issues that could manifest themselves in a very negative way," Riley patiently states, watching John fidget constantly, like he's uncomfortable in his own skin.

"If that's what this is all about, to gauge whether or not I'm suicidal, I can guarantee you, Dr. Keller and Woolsey that I am not, nor have I ever entertained thoughts of killing myself," John says emphatically as Riley gestures him to keep walking.

"Like I said, I read your file Colonel and I've read you're mission reports. You have a knack, for shall we say, putting yourself in situations that have had a degree of certainty you couldn't get out of. Like single-handedly dealing with sixty Genii soldiers by yourself. Flying a Puddle Jumper with a nuclear warhead in it to detonate in a Wraith Hive ship. Breaching quarantine around Dr. Weir and touching her while her body was heavily infected with nanites. Persuading Dr. Keller to patch you up just enough so you could go after Teyla Emmagan instead of having surgery and letting someone healthy go after her. Most recently slamming a Puddle Jumper into the Tower of Atlantis and going into the Isolation chamber while Dr. Keller was infected with what was the beginning of a Wraith Hive ship to inject a phage into her without back up and not even knowing if it would work or not, and my personal favorite, disobeying a direct order from not only General Landry but General O'Neill as well, to rescue Mr. Woolsey and General O'Neill. Can you maybe see where the concern might come from Colonel?"

"You forgot single-handedly trying to help McKay ascend, that was no picnic," John says, trying to add some humor to the conversation.

"Do you really want me to list off all the times you've single-handedly gone after not only your team members but many of the other civilians in this City?" Riley smiles at John as the door to the pier opens and John gestures the doctor to precede him outside into the warm air and sunshine.

"No, no that's not necessary and as far as doing my job, I'd do any of those things again for any one of my family… uh, team," John says getting defensive about his past actions, as he always does.

"You see your team as family?"

"Yeah, in a weird 'we've all been thrown together to survive' kind of way," John says nervously, scrubbing the back of his neck.

"Have you ever thought of telling them?" Riley asks while she and John sit on the edge of the pier and John looks over the water.

"I…I told Teyla once. We were going to get Ronon back after he'd been captured, given back to the Wraith and made a Runner again. We were on the Daedalus and she came to thank me for going after Ronon even though we'd only known him a year. Like I told her, they are the closest thing I've got to a family and I'd die for any of them." John averts his eyes away from the woman next to him.

"Have you ever told Ronon or Dr. McKay?"

"In my own way, yeah. We're not exactly what you'd call vocal about…"

"Anything emotional?" Riley supplies with a knowing smile.

"Yeah I guess."

"Did you ever tell Lieutenant Ford or Dr. Weir that?" Riley quietly asks, waiting for the Colonel to throw her into the water below, knowing she's hit a sore subject, or two.

"No, I never did. I never got the privilege," John says in a whisper, his head hanging a little lower.

"So this A.I. said you torture yourself everyday. Do you think there's any credence to that?"

"We don't leave our people behind, it's that simple."

"But it is something you think a lot about, isn't it Colonel?" Riley asks while John looks at her with eyes blazing.

"Not a day goes by Doctor, not a day."

"Can you think of a reason as to why the A.I. would have chosen I believe the man's name was…?"

"Kolya, Acastus Kolya." John supplies the name quietly. "Yeah I've got an idea or two."

"Care to share?"

"Do I have a choice?" The anger evident in the whisper.

"Of course you do, Colonel; I already told you that I planned to clear you for duty. You can get up any time you want and go about your day," Riley says, watching John's body language change in an instant.

"Seriously?"

"Seriously. You're the only one controlling this; I'm just a sounding board at this point."

"Then if you don't mind, I do have better things to do. Like sit in an Ancient Chair for the rest of the afternoon," John says happily with a smile, standing and then helping Riley to her feet.

"Then I bid you good day, Colonel and please remember my door is always open."

"Don't take this the wrong way Doctor, but I don't plan on ever knowing where your office is."

"None taken, but we will see each other from time to time and I hope you won't make me pretend to not know you."

"Would a nod and smile suffice?"

"Certainly, I always have a smile for anyone willing to accept it."

"And a beautiful one at that, uh…I really should go," John says easily and then, suddenly realizing he is flirting with the City's psychologist, shakes his head to clear it.

"Yes, your throne awaits."

"My throne…that's good. I think I'll have to share that with McKay, you know for bonding purposes." John turns, tapping his comm. "Rodney? You still want to do those tests?"

"_Of course."_

"Let me take a shower and I'll be right there."

"_A shower?"_

"Yes. I've been out in the sun, I'm sweaty and sticky and I'd like to change into a fresh uniform."

Riley smiles, hearing John say something about kirking. Realizing she should be having a conversation of her own taps her comm. "Mr. Woolsey this is Dr. Kwiatkowski. Do you and Dr. Keller have a moment?"

While John walks into the City he suddenly notices that McKay is breathing heavily into his comm.

John hears the distinctive crack of bantos sticks hitting each other. "McKay, did I call at a bad time?"

"_No… why would you say that?"_ Rodney pants.

"Cause you sound distracted."

"_Just getting some exercise."_

"Are you sparring…with Ronon?" John questions, hearing the Satedan grunt in the background.

"No, it's Teyla," Rodney says sarcastically, ducking a blow with more luck than skill.

"So I'm Don Quixote, but you're Jackie Chan?" Sheppard asks irritably, stopping in a hallway. "You do know he's gonna hurt you, he always does."

"_Not this time. My eyes are straight ahead. I am focused on him. I'm not taking my eyes off him…"_

Suddenly there is a cracking sound, a thwack and a groan…followed by a low chuckle.

"It still didn't work did it?" John inquires with cynical innocence.

"_What makes you say that?"_ Rodney rasps out over the comm link.

"Well, I know you haven't been practicing and I also know that Ronon practices every day, add that to…"

"_Yes, yes get on with it."_

"…The fact that you sound just more than severely winded, leads me to believe that you're probably on the floor right now," John finishes with a self-satisfying grin.

"The great Sherlock Holmes has spoken. Can we maybe just skip this and move onto the tests?" Rodney says angrily while Ronon helps him up.

John hears Ronon ask, _"Who's Sherlock Holmes?"_ Chucking aloud. "Coulda been Mensa ya know. I'll meet you in the Chair Room, Sheppard out."

Walking to his quarters, John remembers where he first told Rodney about his taking the Mensa test, passing but never joining. "It was almost four years ago. Wow time really is flyin', it feels like yesterday," John says to himself, recalling he and Rodney arguing over the pedestal in the underground bunker on Dagan that belonged to the Brotherhood of 15.

"_The numbers one to nine have been put in three by three grids with fifteen in every direction," John says suddenly while Rodney looks over his shoulder._

"_Oh you're right…how'd you know that?"_

_John smiles almost maniacally at the idea of not dying, "It was on a Mensa test."_

_Rodney looks at his in disbelief, "You're a member of Mensa?"_

"_No, but I took the test."_

_Suddenly Rodney's face becomes deadly serious. "When?"_

_John looks up at Rodney realizing the doctor is serious, "You wanna talk about this now Rodney?"_

_The astrophysicist realizes that they are still in mortal peril, "Right, right..." looking over at Kolya and then back at the pedestal, "Okay."_

_While Rodney puts the stones in place John starts to calculate, "two…nine…four"_

"_Seven…five…three…six…one…eight, that's it, that's gotta be it," Rodney says somewhat excited, looking at John who is smiling stupidly at the stones._

"_Good luck," John hears Kolya say somewhere next to him._

Shaking his head to release the memories, John can't help but think to all the other times Kolya was a pain in Atlantis' side. "More than that, he was a pain in the ass," John mutters, reaching his quarters, stepping inside and yanking his shirt over his head as another memory stares back at him in the mirror.

"_I thought you said this wasn't personal," John says, after being shoved into a chair and handcuffed._

"_The truth is, I would've settled for Dr. McKay, but I don't imagine I would enjoy his constant wailing," the disgraced Genii Commander admits coldly, not making John feel any better about the situation he is in._

"_They're never gonna make the trade Kolya. Why don't you just finish this?"_

_Kolya doesn't hesitate for a moment, "I think you underestimate the sympathetic nature of Dr. Weir."_

_John speaks almost on top of Kolya, "Well then, you underestimate Elizabeth."_

The name snaps John out of his memories. He steps into the shower and under the warm water.

"I don't think I ever thanked her for what she did for me, what she wanted to do for me. Kolya underestimated her then and during the storm. He never learned that she was so much stronger than he ever gave her credit for," John murmurs to the thin air around him while his mind floods with memories of the great storm that hit Atlantis only two months after they first set foot in the City. And if that wasn't enough to deal with it was also the first time they met Kolya.

_Kolya holds the radio up to talk. "You killed two of my men."_

_The strong winds make it so John has to yell over the radio. "I guess we're even."_

_Kolya yanks his gun from inside his coat. "I don't like even," he says angrily, cocking the pistol._

"_I'm not finished yet," John yells, watching the rain approaching._

"_Neither am I. Say goodbye to Dr. Weir," Kolya points the pistol at Elizabeth while all Rodney can do is watch, clutching his wounded arm._

"_The City has a self-destruct button. You hurt her I'll activate it, nobody'll get Atlantis." John yells into the radio, going to the most extreme measure he can think of._

_Kolya keeps the gun trained on Elizabeth. "Even if it exists Major you need at least two senior personnel to activate it…and I'm about to take one of them out of the equation."_

"_Kolya?...Kolya?" Without an answer John rethinks his position, it only takes him the blink of an eye to make his decision. "I'll give you a ship, I'll fly it out of here for you myself," John concedes, trading himself for Elizabeth. But there is no answer from the other end of the radio. "Kolya?" John yells feeling something breaking loose inside of him. "Kolya…Kolya don't do this."_

As the memories play out in John's head; the City begins reacting to his thoughts and the temperature of the shower starts to climb. But John doesn't realize it; he is too lost in his thoughts and memories.

"_Major Sheppard, how's this for credibility, Weir is dead."_

_Without hesitation John reacts, "I…am going…to kill you."_

"_Maybe. Stay out of my way, or McKay'll join her."_

_With those three words Kolya had managed to snap what little self-control John had left. He left the grounding station knowing what he has to do. He will never let the Genii have the City. Elizabeth would not want that to happen under any circumstances. Giving a silent apology to McKay, John starts stalking Kolya's men, knowing his actions might anger the Commander enough to make good on his last threat._

_After killing three more men John asks himself "What would McKay do?" Then it comes to him; cut the power and take back the Control Room, especially after hearing the Genii soldiers can no longer track him and there are reinforcements coming._

_There is a part of him that thinks twice about what he needs to do, but that's not the part that is governing him now. He barely hesitates knocking Radim unconscious, sliding him to the floor. Then he steps back to the console that controls the Gate, hitting the button that brings up the Gate's shield, knowing he is killing a large number of men by doing so. As Sora realizes what he has done John sprays the Gate Room with a hail of bullets, covering himself as he takes off down the back stairs._

_Suddenly he hears a voice he didn't think he'd hear again._

"_Major Sheppard I have a proposition for you," Kolya speaks over his comm link._

_John runs out of the hallway he is in and down some utility stairs so the Genii that are nearby can't hear him. "Kolya, I'm having a hard time keepin' up, what's the score again?"_

_After Kolya informs John that he doesn't believe for one second that Sheppard would rather destroy the City than let it fall into Genii hands that if he were to determine that Atlantis was more trouble than She was worth, in Kolya's words "Doctors Weir and McKay would become obsolete."_

_Suddenly the rage inside John stalls for a moment, "Weir's alive?"_

"_Dr. McKay was able to make a strong case for keeping her alive."_

"_Let me talk to her."_

_Suddenly John hears, "Sheppard, we're both here."_

"_It's good to hear your voice," John says warmly as the vengeance begins to slide back into its cage, but only slightly._

"_Yeah, it's good to hear." _

_Then John hears Kolya. "We have less than one hour before the storm hits full force, if the power is not returned to grounding station three within the next ten minutes Dr. Weir dies." _

_John rolls his eyes, "Again you mean."_

_After giving Sheppard the full ultimatum that McKay will die ten minutes after Elizabeth and the Genii will leave with what they came with and leave the City to be destroyed, John begins retracing his way back to the generators he disabled._

"At least I was able to get the power back on in time," John muses aloud. "With a little help from Ford, Carson and Teyla."

_As the team make their way to the Control Room Ford questions the smartness of doing so._

"_As the shield goes up over the City, Weir and McKay are expendable to Kolya. We gotta take the Control Room first," John replies._

_Teyla questions him next. "Would he really kill them just because they are of no further use to him?"_

"_No he'd kill them to punish me."_

_Somehow Elizabeth had convinced Kolya that Atlantis wasn't worth the trouble because suddenly John and Ford see the Gate activate and the Genii soldiers taking their gear back through._

"_Change of plans, you got McKay," he says, seeing the rest of the men-including Kolya, with an arm wrapped around Elizabeth._

_They open fire on the remaining men as McKay manages to get to safety behind Ford, but Elizabeth isn't so lucky. Kolya manages to get her in front of him as a human shield and begins backing to the open wormhole._

"_You're not goin' anywhere," John feels the deadly solider in him step forward. "I will shoot you if you don't let her go."_

"_And risk hurting Doctor Weir?"_

"_I'm not aiming at her," comes the monotone answer. _

_The force of the shot propels Kolya back, forcing him to let go of Elizabeth and she manages to throw herself to the side as Kolya fell back through the Gate and out of sight._

"I scared the crap out of her that day; she saw a side of me I hoped never to have to show her. But I also showed her exactly what I would do for not just the safety of the City but her and Rodney as well. I just wish I never would've seen what she was capable of doing for not just the safety of the City but for all of us," John mumbles, leaning all his weight forward and hanging his head under the water. Then suddenly his rage boils over, pulling back and punching his shower wall with his right. Suddenly the water that was a little on the warm side turns boiling hot, spewing all over John's neck and back.

"Ahh." John jumps out of the stall as quickly as he can without getting any more of himself burned. "That's gonna leave a mark." Surveying his back in the mirror as best he can, seeing angry red blisters already forming.

"What was that?" Ronon asks, hearing Rodney's ever present tablet computer beep.

"There was another power spike; this one came from…Sheppard's quarters?"

Ronon turns and breaks into a run to his team leader's quarters, hitting his comm. "Sheppard are you okay?"

"_Yeah I'm fantastic."_ Rodney hears over his radio as he and Ronon rush to John's quarters. "What happened?" he asks, looking at the information on his computer.

"_The damn shower scalded me. What is going on around here Rodney?"_ John grinds out.

"I have no idea. Power's been spiking all over the City. This is the first time I've been able to pinpoint it to a specific place," Rodney says irritated, pecking away on his computer pad.

Suddenly the Satedan stops moving, processing what Rodney has said.

"What if the power spikes have something to do with Sheppard?" he asks abruptly as Rodney realizes he's five paces in front of the big man.

"What? Like he's causing them? How is that even possible?" Rodney asks with Ronon looking down at him.

"I don't know. You're the scientist you figure it out."

"Oh why I ever listen to you is beyond me. Just because the spike came from Sheppard's quarters doesn't mean he has anything to do with it," Rodney snaps at the Satedan.

"I'm not saying he's the cause, but maybe he's connected in some way."

"Listen, just stop talking. I've got to figure out a way to shut down the alarms," Rodney's impatience takes over and he begins walking again.

Ronon and Rodney stop at John's door. "You decent Sheppard cause we're comin' in."

It opens at John's mere thought, "Listen I told you guys…"

"What the hell happened to you?" Rodney asks in a gasp, seeing John's back.

"What?" John asks as he tries to twist around to see his back but ends up wincing in pain. "Oww."

"Yeah I would think so. You have maybe third or fourth degree burns on your neck and back. We need you to get you to the Infirmary, now," Rodney steps closer to get a better look at the red blistered skin of his best friend.

"Rodney, stop being a hypochondriac. It's just a little tender," John says admonishingly, trying to put a T-shirt on. "Oww! Okay, maybe we should go see Keller, just to make sure."

"Trust me, you're gonna thank me."

"Somehow I doubt that Rodney."

Ronon just chuckles, following his teammates out of John's quarters.

"What have we here? Rodney what's wrong? Are you feeling okay?" Jennifer asks when she sees Rodney walk into the Infirmary with Ronon behind him.

"What? Me? I'm…I'm fine. No it's not me that we're here for," Rodney turns to gesture to John only to find Ronon standing behind him. "What? Not him either, it's Sheppard. Oh for God's sake! Let her look at you. It could get infected and you could get blood poisoning." Jennifer sees Rodney talking behind Ronon.

Leaning to one side she sees a shirtless John looking back at her innocently.

"Just a little accident in the shower, nothing to worry about."

"Why don't you let the doctor determine that," Rodney snaps out, concerned for his friend.

John sits on a diagnostic bed while Jennifer pulls on surgical gloves. "This from the man who thinks medicine ranks just above voodoo as a science," he jabs back.

"What happened?" she asks, gently pushing on some of John's skin that is blistering.

"Ahh, the shower scalded me. I tried to think it cool but it didn't work," John supplies while Jennifer looks at his neck as well.

"I was thinking third or fourth degree burns, since it blistered so quickly," Rodney says, turning to Jennifer while Ronon and John roll their eyes.

"Not quite, but it was quick thinking not letting him put a shirt on and getting him here as quickly as possible." Jennifer smiles at Rodney, his cheeks turning pink from the attention.

"Yes well, he is a team member and a vital member of this expedition. We need to make sure he's in tip top shape," Rodney rocks back and forth on his heels, grinning as John looks at him slowly.

"That he is," Jennifer replies, turning to John. "Colonel, I'm gonna ask you to lie on your stomach. I need to disinfect the open blisters to stop infection and dress the wounds. This might hurt; would you like something to take the edge off?"

John raises his eyebrows at the doctor without uttering a word.

"Okay, just thought I'd ask." Jennifer grabs a bottle of antiseptic, some cotton swabs and gauze while John deals with the pain of shifting around on the bed.

"You know you guys don't need to hang around and watch her…ahhck…do this….oh wow, that's….eye watering," John says looking at Ronon and Rodney, then feeling the first sting of the antiseptic.

"We'll stick around and walk you to the Chair Room." Rodney says, jumping up on adjacent bed. "Just to make sure you make it there in one piece."

"Colonel Sheppard's not going anywhere for the time being. At least the next few hours." Jennifer looks at Rodney, making him frown deeply with her comment. "I would like to be able to monitor your wounds. Just for a few hours, make sure no infection sets in," she adds, addressing John when he raises his head.

"Can't I at least go back to my quarters?" John asks plaintively.

"In a few hours. There was nothing pressing that needed your attention was there?"

"Oh no, nothing important, just testing to make sure the Chair was working properly. Hopefully the Wraith won't attack any time soon, or those evil Asgard that are unaccounted for." Rodney sighs in resignation.

"Good to know," Jennifer says ignoring everything Rodney said except the first four words. "He'll be able to light things up for you tomorrow, Rodney. Right now I want the Colonel here, so if you and Ronon have something better to do I suggest you go, unless you want to keep the Colonel company for the next four hours." John and Ronon look from Keller to Rodney and then at each other in amazement.

"I guess I could go back to my lab and try to figure out these four power spikes," Rodney admits in quiet dejectedness.

"Four?" John lifts his head up yet again, wincing as he kinks his neck. "I thought there were only three."

"Zelenka found one that happened about 0500," Rodney says, getting excited. "See we set up this program to scan for spikes of power. Granted it wasn't as huge as the last one, but it seemed to fit the program's parameters…." His voice trails off seeing three sets of eyes looking at him expectantly.

"So, have you been able to figure anything else out?" John asks sarcastically, bordering on condescending.

"Well no…not yet. We don't have any more information."

"Well I suggest you find some," John demands. "What if the next spike releases Halon gas or something equally as toxic or sends a beacon that alerts the entire galaxy of our location?" he asks angrily.

"Fine." Rodney slips off the bed, looking at Jennifer. "Don't be afraid to use the extra long, extra sharp needles on Colonel Cranky-Pants here."

As Rodney leaves the Infirmary Ronon takes a last look at John and follows in Rodney's wake.

"Hey McKay, wait up! McKay, I got a question for you. What time did you say the first spike happened?" Ronon asks, catching up with Rodney.

Rodney turns to face his teammate. "0500, why?" He asks snappishly.

"I was out for my run…"

"Well good for you, is this some sort of dig on my physical shape because I will have you know…"

"McKay, stop talking and listen for a minute," Ronon snaps out, getting Rodney to stop and pay attention. "I take the same route every morning; I was going by the personal quarters at that time."

"What does--?" Rodney starts.

"I was running by Sheppard's quarters and I heard something break, like glass. I couldn't find the source of it but the lights flickered for a second. I was talking to Teyla before and she was up with Torren at the same time and she noticed the lights too."

"You heard glass breaking and you think the power spikes might have something to do with it. Gee let's alert the media, I think you might have cracked the case." Rodney looks up mockingly at Ronon.

"It wasn't just me, Teyla saw it too." Ronon takes a step closer to Rodney.

"Oh alright, we'll go check it out. I wouldn't want to get my ass kicked unnecessarily…again," Rodney concedes. He and Ronon walk to a transporter to take them to the part of the City where some of the personal quarters are.

"So Doc, when am I gonna be able to get back to active duty?" John asks while Jennifer finishes the last of the bandages on his back.

"Well, I was gonna put you back on today but with injuries like this, it's gonna be another couple of days. Don't worry, Colonel; it's purely a physical setback. Dr. Kwiatkowski gave Mr. Woolsey and I her recommendation just before you got here. She cleared you with flying colors. Now just lay there and relax, I'll come check on you in a little while. Do you want your Gameboy or something?" Jennifer asks, bending down so John doesn't have to move his neck.

"No I'm fine, I'll just lay here. Thanks Doc, I appreciate all this," John says, cocking a thumb to his back.

"All part of the job Colonel, now rest. You'll be back in your quarters in no time."

Ronon and Rodney step out of the transporter and walk the long hall to John's quarters. "Okay here we are. Where were you when you heard the crack?" Rodney asks, watching Ronon point to the right hand side of the entry-like space outside John's quarters. "So if you heard it up there that means that taking acoustics into play it should have happened over here." Rodney points to his left and behind them as Ronon shakes his head.

"I already looked. That was the first place I checked, but nothing's broken. So I looked everywhere, nothing's broken, nothing's cracked, nothing's missing." Ronon crosses his arms and stands in the middle of the large space watching Rodney circle around him while the scientist's eyes are glued to the floor looking for stray pieces of glass or something broken. "If I can't find anything, what makes you think you'll do any better?" Ronon asks, feeling like Rodney doesn't trust him or believe him. "Do you want me to get Teyla so she can tell you what she saw?"

"No, no I'm sure you both thought you saw the lights flicker and I'm sure you thought you heard something like glass breaking, but I'm not finding any evidence," Rodney says, wanting to believe his teammates. "At least it would give me a straw to grasp at," he mutters to himself, feeling his frown deepen.

"What if I heard it wrong, what if what I heard came from in there?" Ronon looks straight ahead of himself at John's door.

"In there? Anything that you would have heard out here would have been loud enough for Sheppard to hear, even in a dead sleep. It would've woken him up and he would have remembered, but he hasn't said anything," Rodney counters Ronon's thought.

"Let's take a look anyway."

"What? That's breaking and entering," Rodney looks indignantly at Ronon. "We can't do that."

"Then ask him?"

"What am I supposed to say? Excuse me Colonel Grumpy, Ronon's been hearing cracking noises and he thinks they're coming from inside your quarters, but he doesn't think you'd hear it," Rodney says sarcastically looking up at Ronon.

"How about tellin' him you want to check out his shower, to see why it scalded him so bad," Ronon rolls his eyes at McKay.

Rodney does a double take. "Hey, that could work" he taps his comm. "Sheppard come in."

"_Yeah McKay, what'cha want now?"_

"I want to look at your shower unit to see if there was anything malfunctioning," Rodney says, waiting to hear Sheppard tell him to bugger off.

"_That's a good idea Rodney. Go ahead it's not locked." _

"I'll make sure it is when I leave, if you're not back, McKay out."

"See, was that so hard?" Ronon asks, slapping Rodney on the back.

"Yeah well let's get in and out…"

"McKay, over here." Ronon walks over to the windows that are parallel to John's twin bed.

As Rodney walks closer to the windows he can plainly see what Ronon is pointing at. "My God." Both windows have multiple spider cracks running through them.

"And because it's such a wide open space the noise would be louder than normal and you'd be able to hear it, especially if you were that close to the door and walls," Rodney says, turning on the flashlight he has with him and shining it on the entire length of the windows, which are good two feet over his head. "But how was he able to sleep through this. There's no way he wouldn't have heard this happening?" Rodney questions while Ronon looks around to see if anything else is amiss.

"I got nothing, let's check the shower out."

"Yeah sure," Rodney backs away from the windows, totally distracted by what he sees.

"Did Sheppard say anything about his hand hurting?" Ronon asks as Rodney steps into the bathroom.

"Not that I heard. Why?" Rodney asks, looking around Ronon's big frame and into the shower. "Oh crap. What is going on?" Rodney gasps at the sight in front of him. At chest level there is an indentation in the wall the size of Sheppard's fist, with spider cracks emanating from the initial hit. "Sheppard this is McKay come in."

"_What is it now Rodney? You wanna raid the fridge?"_ comes the sarcastic question.

"What?…No! I was wondering how your right hand feels?" Rodney asks shaking his head, as Sheppard's question throws him off balance.

John lifts his right hand, flexing it slowly and trying not to grit his teeth too loudly. "It feels fine."

"You sure?"

"_I think I would know Rodney. What's with the twenty questions?"_

"Oh, no reason. You just have a small crater in your shower wall and did you know that both your windows have multiple cracks in them as well," Rodney says, talking to the ceiling.

"What? Oww," John exclaims, trying to fully sit up, stretching his neck and back in the process.

"Are you okay?" Rodney asks, hearing John's outburst of pain.

"_I'm fine Rodney. How the hell did I get cracks in my windows?"_ John asks calm one moment and frustrated the next.

Rodney, hearing the difference snipes back accordingly. "I don't know yet, Colonel Schizoid. I'll get back to you." He taps his comm closed so he has no idea what John says in return.

"What's a schizoid?" Ronon asks. He and Rodney look around to make sure nothing else in the Colonel's quarters is damaged.

"It's not a thing, it's short for schizophrenia, a mental disorder…a disorder of the brain," Rodney explains while Ronon looks at him, brows knitted together in puzzlement.

"Could that be what's wrong with him?"

"I don't know. There's no definitive test that can be done to determine it. But then again, five years in this place would turn anyone schizoid."

"Well, something's going on with him," Ronon says simply, Rodney turns to him in frustration.

"I know that."

"Then fix him."

"I don't…know how." Rodney's shoulders slump. "I can't even begin to know what's wrong with him."

"You can add lying to the list," a soft voice comes from the doorway.

Both Ronon and Rodney jump in surprise as Teyla steps forward to examine the crater in the shower wall.

"I am certain that Colonel Sheppard would have hurt his hand with a punch like that. A mere tap or even a strike at half force wouldn't have caused that much damage. This was a strike at full force; the Colonel would have had to be very angry to inflict this and would most certainly have hurt his hand." Teyla addresses her teammates, stepping back.

Rodney looks at her with a half smile of condescension on his face. "How can you tell that from a hole in the wall?"

"Are you going to replace this panel before Colonel Sheppard returns?" Teyla asks calmly, used to Rodney's behavior.

"Yeah, I can get a team…"

With a slight nod from Teyla, Ronon lunges forward, punching the wall next to him, immediately grimacing in pain.

"Hey, hey! Now they'll have to do both walls! Wait, there's cracks, but no crater," Rodney says, looking closely at the wall, and then to Ronon. "How's your hand? Anything broken?"

"No, but it stung, that's for sure," Ronon says flexing his fingers one at a time then rubbing his knuckles.

"Now we know Colonel Sheppard would have most definitely hurt his hand," Teyla states simply.

Rodney looks at her confused. "But then why did he sound so surprised when we said there was a hole in his shower wall?"

"Maybe he didn't know he hit it."

"How could he not know, Iron Man? You barely dented it and he was able to break it; that makes no sense."

"What if the power spike had something to do with it?" Teyla asks as both men look at her.

"Like what? It gave him the power to smash the wall without smashing his hand to pieces? I can't even begin to imagine how that could be done," Rodney says dumbstruck.

Ronon clasps a hand on his shoulder. "You might have to," comes the low, rumbling reply.

"Hey Doc! It's been four hours; can I please get out of here?" John asks loudly, spying Jennifer off to the side of the large Infirmary.

"Let me take a look at your back and we'll see," Jennifer answers, snapping on surgical gloves and begins to pull some of the loose bandages away to look at John's blistered back. "Well things look good for now. I want you here first thing tomorrow morning so I can change the dressings and maybe even put something a little more firm against your skin." Keller advises, pulling out a double blister pack of pills, handing them to John. "I want you to take these tonight."

"I don't need pain pills Doc; it really doesn't hurt…much"

"They're sleeping pills. You have to sleep on your stomach tonight and these will ensure you get a deep enough sleep that you shouldn't flip around. Just to be sure, put a pillow on either side of you that way your body should stay prone," Jennifer pulls John's right hand up and slaps the pills into it playfully.

As her grip on his hand firms, John cannot stop the hiss of pain that passes through his teeth.

"What's wrong? Your back?" Jennifer moves to look over John's shoulder at the dressings but still having a hold on his hand. He tries to pull away but it brings another grunt.

"What happened to your hand? It's slightly swollen across the knuckles," Jennifer examines John's right hand, flexing the fingers to make sure they're not broken. "I'd like to get an x-ray to make sure the carpal and metacarpal bones aren't broken," she says as John's questioning eyes make her smile while helping him get situated in the right position. "The bones in your hand, I can tell by the feel and sight that your phalanges aren't broken, but I can't tell about the bones up here," the doctor explains, tapping on the top of John's hand.

"Gotcha. Well, I can say they don't feel broken. I don't even remember hurting myself, I don't know when…" John says as suddenly he has a flash of memory hitting the shower wall and the water turning boiling hot on his back.

"Colonel? Colonel are you okay?" Jennifer asks when John drifts off in mid-sentence.

"Yeah, just thinkin' it'd be nice to get outta here and back to my quarters."

"Well, that can be arranged. Give me a minute to look at the x-rays, but I think you're fine."

"Thanks Doc, I appreciate it," John says. His comm beeps. "Sheppard here."

"_Just wanted to let you know that the techs have replaced your shower wall so you'd never know there was a hole and I couldn't find anything wrong with the system, at least on this end,"_ McKay says somewhat distracted-sounding, tapping away on his tablet computer.

"So what the hell caused the spike?" John asks getting irritated with Rodney.

"_I don't know,"_ McKay says slowly on purpose. _"I haven't gotten the results from the other systems yet, but I thought you'd be happy to know you can use your shower in the morning so you won't have to bum off me or Ronon."_

"I'll be happy when you figure out where all these power spikes are coming from."

"_Yes, yes I know and hopefully I will have something for you in the morning,"_ McKay snaps back, getting defensive yet again.

"Hopefully? You don't know? You're slippin' big time McKay,"

"_I am not. The systems are reacting incredibly slow for some reason. I'm not getting readings from some systems and wildly inaccurate ones from others. It's like the City is trying to keep me guessing and won't let me get a solid fix on the problem."_

"Why?"

"_If I knew I would tell you,"_ McKay says, enunciating every word slowly before tapping his comm off.

"What did I tell you? He's acting weird, it's like he's angry all the time," Ronon says looking to Teyla who turns to McKay.

"Rodney, are you all right? You do not look well." Teyla puts a comforting hand on McKay's arm.

"Yeah I'm fine, I'm gonna head back to my lab and see if I can come up with anything. Buzz if you need me," the scientist says quietly, walking out of his best friend's quarters, feeling inadequate.

"Well Colonel, you're outta here. The x-rays look fine. You're probably gonna have a heck of a bruise on that hand for the next few weeks, but nothing that's gonna keep you from active duty," Jennifer says walking over to the bed that John is laying face down on. "Just be careful please." Helping John to his feet and put his shirt on. "I would like to go one day without having to treat you for something."

John takes a huge breath to calm himself. "I'll try Doc, but no promises." Trying to sound flippant, it comes out sounding nasty, even to him.

"Take it easy and be careful taking a shower tomorrow. Try not to get your back wet, and don't forget to take the pills I gave you. If you want you can take them now, they'll help you sleep a lot more comfortably," Jennifer advises.

John shakes his head. "It's still early. I'll take 'em in a little while, closer to my bed time." John turns and starts to walk out the door. "Thanks Doc, see ya tomorrow," he calls over his shoulder.

"So, you think the City is affecting Colonel Sheppard somehow?" Woolsey asks, circling his desk, stopping to stand behind his chair to face Ronon, Teyla and Rodney.

"_T__hey_ do," Rodney says, glancing up from his computer to see the expedition leader looking at him. "I'm…I'm just here for moral support."

"Moral support?" Woolsey questions.

"Of course, he's a part of our team. I thought I should be here to show my support for my team members." Rodney defends himself as three sets of eyes focus on him.

"Anyway, how can the City be affecting Colonel Sheppard?" Woolsey shakes his head, posing the question to Ronon and Teyla.

"It has been long believed among my people that anyone who possesses the Ancient gene can talk to the City, as it were." Teyla explains.

Rodney takes his turn to shake his head. "We already know he can do that. He can open doors, turn lights on, turn consoles on all with just his mind, not to mention the Chair," Rodney says, conceding that point.

"But my people believe it is more than that. Some of the elders believed that anyone with the Ancient gene had the ability to connect with the City in every way."

"And you think Colonel Sheppard's able to do that?" Woolsey sits down in his chair and leans over his desk. "Dr. McKay, is something like that even possible?"

"I'm sorry, what? Look, there is no way that Sheppard could be linked with the City like that," McKay says sounding skeptical, almost to the point of being condescending.

"Why not?" Ronon asks.

"Because then I'd be able to do it as well," he says, pointing to himself. "Hello, I've had the gene therapy and I can't link to the City."

Ronon looks at him with a small smile, "Have you ever tried?" he asks, baiting Rodney.

"Well…no, no I haven't," he admits as everyone looks at him. "What? Do you want me to try?"

Woolsey shakes his head at Rodney. "Could it be that you need to have the pure gene and not the therapy? Maybe the City can tell the difference?"

"That very well could have something to do with it, couldn't it Rodney?" Teyla asks as Rodney looks up again.

"I honestly don't know. Why don't we ask Sheppard himself and see what he says? I've never heard of anything like this and if it needs the pure gene to communicate, you can't get any purer or stronger than Sheppard's."

"It's my understanding Colonel Sheppard is not on active duty due to his injury to his neck and back. I suggest we watch him and if any more suspicious behavior or power spikes occur we take more active steps to figure out what's going on. For now, Dr. McKay, please keep working on what the power spikes are and where they are coming from, or if it happens, from whom?" Woolsey says as Ronon, Teyla and Rodney get to their feet to leave the leader's office.

Meanwhile John has gotten back to his quarters after a stop in the mess for a late dinner. "Wow, how the heck did I miss those?" John asks himself, looking at his windows and seeing multiply spider cracks in the large windows. "And what is with all the safety tape, McKay?" He muses, touching the six pieces of yellow and black safety tape that run the length and width of each of his windows. "What does he think I'm gonna do, jump? Trust me, I learned my lesson the last time I tried to pick a fight with a window…granted the window was dust, but I wasn't exactly human either," he says, remembering a conversation with Elizabeth in her office, and the outcome.

_Elizabeth walks into her office, examining a book of Ancient text. Turning to sit down she hears a familiar voice._

"_Look," John says, artificially happy, pointing over his shoulder at his Marine escort. "I made a new friend."_

"_It's only protocol," Elizabeth promises, putting the text down on her desk._

"_That's your answer for everything," John replies challengingly, keeping eye contact with Elizabeth._

_Breaking it first, she looks down at his mutating right hand, "You look well."_

_John, realizing Elizabeth is looking at his hand, shoves it in his pocket self-consciously._

"_Should you be out of bed?"_

_John turns to Elizabeth's desk and she can see the mutation creeping up the right side of his neck. "I was goin' a little crazy down there so they said I could walk around for a bit."_

_Elizabeth smiles encouragingly, "That's good."_

"_Yeah," John brings his gaze back up to Elizabeth's face, knowing she is as uncomfortable as he is._

_They both exhale, looking for something to say. John is the first one to find his voice. _

_Taking a step toward Elizabeth he says in a quiet voice "Look, what I'm tryin' to say is that I want to go on this mission."_

_Feeling like she still has her second-in-command in her office, she ventures forward a step as well. "Hey you said it yourself; you are not fit for any off-world activity."_

_John nods his head a beat and then looks back up, straight at Elizabeth. "The inhibitor that Beckett's got me on, the one that's keeping me lucid, they keep having to up the dose."_

_Elizabeth looks away, not wanting to show John the defeat she is feeling. "I know, they told me."_

_John can feel the anger welling inside of him at Elizabeth and it's making him clench his teeth. "I don't know how much time I have, but the last thing I wanna do is sit on my…" Suddenly his right hand, fingers splayed, is in front of their faces and his voice is getting louder, "…Mutating hands while my team puts their lives on the line trying to find me a cure."_

_Elizabeth follows John's hand up and then down again in slight horror at what her friend is becoming._

_John tries again, calmer this time. "I should be with them."_

_Elizabeth takes a breath and looks John in the eyes, "No…I'm sorry."_

"_What's the worst that can happen?" John asks, taking a step or two away from Elizabeth. "I- I…die?"_

"_You could compromise the mission. They have enough things to worry about…"_

_John starts talking over her words, "Whoa whoa, so now what…suddenly I'm a liability?" he asks, stepping toward Elizabeth again._

_Elizabeth stands her ground calmly, "Your condition could change rapidly," she says slowly so John will understand her point._

"_I know," he says as slowly as his voice rises yet again. "And I know I can do this." _

"_I'm glad…you feel that way. But it would be irresponsible of me…"_

_John shakes his head, "This is my life we're talking about."_

_Elizabeth looks straight at John, "I know that."_

_The two leaders stare at each other for a split second and then John decides to try again, without asking._

"_I'm going on that mission."_

_Elizabeth reacts without thinking. "No John, you're not," she says, sounding exasperated and getting fed up with having to belabor the same point._

_Suddenly something snaps in John, the rage he was fighting takes over. Whirling around, "Dammit" putting his fist through the ten-foot tall window behind him, shattering it instantly._

_Before the glass even hits the floor, his Marine escort has the Wraith stunner he is carrying pointed at John. Several people stand up in the Control Room a few stepping forward._

_Elizabeth doesn't hesitate for a moment. "It's okay," she says loudly. Looking at the Marine "Put it down." He instantly lowers the weapon._

_John looks up with a look of disbelief on his face. "I'm bettin' that didn't sell you."_

_Elizabeth shakes her head. "No, no not really." _

_"I should go back to the Infirmary," John states in a monotone._

"_Yes," Elizabeth agrees quickly._

_John's head twitches a little, searching for something else to say. Finally giving up, he steps closer to Elizabeth, avoiding the glass and walking out into the Control Room, leaving Elizabeth to stare at her broken window._

John shakes his head as the memory dissipates. "How you could trust me after that I'll never know. I'm still surprised you didn't open the Gate and send me back to Earth, or at least write me up for insubordination. But then again you'd have told me I wasn't myself and you held no ill will about anything I'd done or said," John whispers, looking out at the moons and then down at the swollen hand that not only broke her window but the hand that also tried to kill her. "Somehow you found the courage to brief me on the mission, never taking your eyes off me as I geared up in the Infirmary, not letting anyone else but Carson in the room with us. You wouldn't even let a security detail walk with us to the Gate Room. You trusted me that much not to flip out on you and Carson." He turns to question the Athosian pot sitting on the table next to his personal refrigerator. "How could you know I needed your faith and trust that badly?"

Not being able to bear not getting an answer any longer John turns back to the window. Shoving his left hand into his BDU pants pocket, feeling an odd object he pulls it out.

"Oh yeah, Keller's sleeping pills. I guess it wouldn't hurt for tonight. I could use a full night's sleep, for a change." John convinces himself to take the pills and walks into his bathroom to get himself a glass of water. Before climbing into bed his gaze falls on the pot across the room as it has every night for the past thirteen months. "Night 'Lizabeth. Your City is safe. We all are," John whispers, carefully getting into bed and promptly falling asleep.

He begins to dream of the trip trough the forest with Rodney and Harmony to the Ruins of Larris.

"_Tell me, which one of you is the superior officer?" young Harmony asks as John and Rodney walk on either side of her._

"_You mean, who outranks who?" McKay asks, trudging along._

"_Yes."_

"_I'm a civilian, I don't have a rank, but basically we're equals," Rodney answers, stepping behind Harmony._

"_Technically I'm in charge," John corrects while Rodney gives him a look._

_The three start to walk single file. "I thought so. You have all the making of an excellent leader John," Harmony says sweetly. _

_John smiles appreciatively "Well thank you."_

_Suddenly something changes around John and he realizes he's alone in the woods. Rodney and Harmony have vanished. As he calls for them he starts to think the worst. "There were Genii chasing us after all," he reasons, starting to look for tracks around him._

_After a while he stops on a boulder to catch his breath and from behind he hears a low chuckle. Before he can even turn he hears a sound like a pulse from a Wraith stunner, and then nothing._

_When he comes to his hands are tied and his feet bound at the ankles. He is quickly able to get free and begins to survey his surroundings._

"_Hello John."_

_John whirls around to find Acastus…"Kolya."_

_Out of the corner of his eye John sees a fist come at him and he is unconscious once again._

_This time when he comes to he finds himself bound to a tree._

"_Not again," John says as everything begins to feel familiar._

"_You have a lesson to learn Johnny boy and I intend to see you learn it," Kolya says, pulling on a pair of leather gloves._

_After the initial blows, John stops feeling the hits that Kolya rains on his face. "I am marveled at how much you can endure," Kolya pants, stopping to see John is still conscious._

"_Well I was married once, and I work with McKay, need I say more?" John tries to be flippant through the blood in his mouth and his swollen eyes._

"_It is of no consequence. I will break you," Kolya promises before leaning over to begin beating John again._

_After a few more minutes Kolya backs off again, wiping his brow on the sleeve of his uniform._

"_Listen why don't you tell me what you want and maybe we can make a bargain. I give you something and you let me go," John says slowly, his jaw and lip swelling._

_He looks up at Kolya but the older man reacts as if he hadn't heard John. "Kolya? Tell me what you want. We once wanted to be allies with the Genii, we still can be. You just need to tell me what you want so I can try to get it for you," John tries to keep his cool and stay calm but the silence from the older man is beginning to unnerve him._

_Suddenly John's surroundings change again and he is now untied but feeling something on his left hand, looks down he sees his hand is gone and is bandaged at the wrist._

"_You're an interesting man Sheppard. You've traveled to another galaxy, risked your life defending a bunch of people you don't even know. But half the time you can't even do that, yet you keep trying and ultimately failing. I've realized it's your past failures that drive you, that keep you from giving up. Hoping that someday you'll get it right," Kolya says, squatting in front of John. "Tell me Sheppard, how is Dr. Weir these days?" the disgraced Genii commander asks with a vengeful smile on his lips._

John lunges for him in the same instant he awakens. "Ahh, dammit that hurts." John pulls a breath in through clenched teeth as his sensitive neck and back complain loudly at the treatment.

Slowly he lays back down, trying to get his breathing under control and flush the memory of Kolya from his mind.

"Okay, time to get up. Gotta go see Keller and get on with my day…in the Chair. Oh, this is gonna be a fun day," John mumbles to himself, carefully getting up. After giving himself a glorified sponge bath and then putting on most of his uniform John tries to figure out how to lace up his boots. "Oh crap."

"Well good morning, Colonel. You look like you got…" Jennifer says, seeing John walk into the Infirmary from a distance, grabbing a tray and walking closer, seeing the look on John's face. "…some rest. What's wrong?"

"I can't get my boots laced. I know it doesn't take much, but it still sucks," John grouses a little as Jennifer sees the laces of John's boots just shoved inside the boot itself.

"Let me look at your back and then I'll lace you up. We can't have you tripping over yourself."

"Thanks Doc," John says, his comm beeping.

"_McKay to Sheppard, are you up yet Colonel?"_ Rodney's voice comes over the comm, sounding a little timid to John.

"Yeah Rodney I'm up and in the Infirmary already. What's up?"

"_I was hoping to finish the tests on the Chair this morning if that's all right with you."_

"What about the power spikes? Have you managed to figure those out yet?" John asks twitching as Keller doctors his back.

"_No I haven't, the computer is still processing data, so I have a few free hours. That's more than enough time to get the diagnostics done on the Chair,"_ Rodney says getting defensive.

"Let me get breakfast and I'll meet you in the Chair Room in an hour or so," John answers while Rodney heaves a sigh of relief.

"_I'll see you then, McKay out."_

"Things are looking good. A few more days and you'll be as good as new. How's the hand feeling?" Jennifer asks finishing with the bandages and watching Sheppard flex his right hand.

"A little stiff. I'll loosen it up later with Ronon." John answers with a smile.

"Be careful. One wrong move and you'll break bones. Maybe you should take it easy on the sparring for the next couple of days," Jennifer advises, patting her knee for John to put his boot on.

"Gotcha Doc. Thanks. Same time tomorrow?"

"You got it. Same time, same place, same routine." Jennifer smiles perkily at John.

"Oh joy, can't wait," John says sarcastically, leaving the Infirmary and making his way to the mess with little incident.

"Colonel, how goes the preparations on the Daedalus?" John asks Colonel Caldwell, who is sitting at one of the outer tables overlooking the water.

He gestures for John to join him. "We should be ready to start taking the non-essential personnel within forty-eight hours if not sooner. The essential personnel will come aboard twelve hours before we head out," Caldwell answers.

"Yeah, McKay's got this presentation he's going to. A bunch of physicists all in one room, downright scary if you ask me," John says taking a sip of his coffee.

"Just to let you know, Colonel, there is still plenty of room for one more if you change your mind."

"I appreciate that Colonel, but I think I'd better stick pretty close to home in case something happens."

"I wonder if Dr. Weir had any inkling how dedicated you'd become to this place when she got you promoted?" Caldwell asks easily with a hint of a smile, taking a sip of his own coffee.

John just about has his own cup up to his lips when Caldwell's words penetrate his brain and he processes what his superior has said.

"What? What did you say, sir?" John asks, wondering if he heard Caldwell right.

"You didn't know? I figured she would have told you; the two of you were so close. I didn't think you had any secrets from each other," Caldwell says, genuinely taken aback.

"No, she never told me. What did you mean by 'she got me promoted'?" John questions, putting his cup down.

"I don't want to say she _forced _General Landry to promote you. She made it very clear that you were Atlantis' Military Commander and if promoting you was the only way for you to stay its commander, then if she needed to, Dr. Weir was prepared to go to the President to make sure it happened," Caldwell explains as John blinks rapidly, stunned beyond words. Caldwell sees the look and confusion creeps into his question. "She never let on? Never hinted?"

"Not to that extent, no. She never let on that she was single-handedly responsible. I knew she must have had something to do with it, but I always thought General O'Neill had something to do with it as well," John admits, remembering back to that late night on board the Daedalus when he found Elizabeth awake and thinking of home.

"I'd better get back to work. Hermoid's been a little testy lately so I have to make sure that the crew is being rotated regularly. Otherwise people start to hear some very interesting language from a supposedly very benevolent being."

"Yeah I'll see ya around Colonel," John says very absent-mindedly. He stands as well and begins walking to the Chair Room, thinking about that night aboard the Daedalus.

_He hadn't been able to sleep, so John thought he'd head to the mess to see if there was any coffee made. He wandered in seeing Elizabeth sitting all by herself, almost looking like she wanted to be left alone. John had noticed that she wasn't wearing the heart pendant she normally wore every day; he wondered if that had anything to do with the doctor she was seeing back on Earth. When he checked his watch, Elizabeth must have sensed him coming because she turned as he reached the table that held the coffee pot and mugs. "Hey, what are you doing up so late?"_

"_Couldn't sleep," John answers while pouring himself coffee and walking over to sit across from Elizabeth. "Must be the uh, burden of command. You know ever since I was promoted to Lieutenant Colonel," he says, trying not to sound too proud of himself, but failing miserably, at least with Elizabeth._

_She smiles at John, attempting to be gracious but having heard the same line over and over again was beginning to wear thin, even for her. "All right John; it's been almost a month. When are you gonna stop trying to find a way to bring that up in every single conversation," she smiles genuinely as she leans forward._

"_You gotta understand," John says, leaning forward himself. "There's a lot of people in the Air Force who never thought I'd make it past Captain."_

"_Well obviously the people whose opinions mattered the most, thought otherwise," Elizabeth says sincerely, looking John straight in the eye._

_As he realizes what she is saying Elizabeth sits back comfortably, raising an amused eyebrow at her second-in-command. John decides not to push, not wanting to know whom she had to blackmail to get him promoted._

"I had no idea she did it all on her own. She believed in me enough to put it all on the line for me and how did I thank her? I let her sacrifice herself not once, not twice, but three times for me and this City, barely putting up a fight in the process," John mumbles to himself, shaking his head, realizing that he is at the Chair Room and he needs a clear head or someone might get hurt.

"Hey Chewy, Teyla. What are you guys doin' here?" John asks, finding his other teammates in the room.

"We just wanted to come and check up on you. To see how you were feeling this morning." Teyla smiles and Ronon nods in agreement.

"Okay Rodney, let's get this done," John says, sitting in the Chair carefully with it automatically lighting up and reclining.

Closing his eyes, John is again swamped with the memory of the last time he used this particular Chair.

"_The angle's too steep. If we keep gong like this we're gonna put too much strain on the shield, which means more power draining from the ZedP.M.," John can hear Rodney answering Teyla's question. "Sheppard we're coming in too steep. You need to ease up on the angle of re-entry."_

_John tries hard to concentrate as he vaguely hears Dr. Lee say something and Sam quiet him. Then he hears Rodney's sharp voice again._

"_Ease up on the angle."_

"_I heard you the first time Rodney," John tries hard to lessen the angle._

"_And yet we're still coming in too steep," Rodney snipes sarcastically, checking his computer._

_John loses himself in trying to ease the angle, but his mind keeps going back to Elizabeth, now alone and in the hands of the Asurans._

_Then Rodney's voice breaks through the fog. "Sheppard, you need to slow us down, we're coming in over the water."_

"_Copy that," John replies vaguely so Rodney knows he's listening._

"_Still too fast! Slow down!" comes Rodney's panicked voice "We wanna touch down gently, like a…like a leaf kissing the surface of a pond."_

"_What is he goin on about?" John thinks to himself, trying to concentrate his energy on slowing the massive City down._

_Suddenly there is impact; John grips the arms of the Chair to keep himself from flying across the room. _

"_Nice kissing." Comes the sarcastic voice of his best friend._

_John sits up with a sigh of relief that at least Rodney is still alive. He turns the Chair off, waiting to hear if they're okay or not._

_"Colonel Sheppard we made it. The City's floating safely on the ocean. Excellent landing," Samantha Carter relays while John shifts in the Chair._

"_Thank you," is all he can manage. His mind is fixated on a figure with auburn hair and blazing green eyes fighting, for the safety of all she believed in and loved._

"Whoa, power levels are starting to climb," Rodney says, tapping away on his tablet.

"Is that bad?" Ronon asks, looking at John in the Chair.

"It could be, there are a number of things he could do wrong in that Chair," Rodney answers, keeping a close eye on his friend.

"Should we consider getting him out of the Chair?" Teyla asks cautiously.

"Not yet, the tests aren't finished and so far everything's okay. If the levels get much higher _then_ we'll have to get him out," Rodney answers vaguely, getting a nod of confirmation from Radek.

"I wonder what he's thinkin' about. It's like he's not even here with us," Ronon says, waving a hand in front of John's face; and John doesn't even flinch.

"_Elizabeth?" John says questioningly, stepping forward seeing Oberoth on his knees holding Elizabeth's wrist._

"_Get to the Jumper," she flings over her shoulder._

_John steps forward again keeping his A.R.G. pointed at Oberoth. "You're coming with us."_

_Ronon leans against the wall as he gets a clean shot at Oberoth but it washes right over the machine._

"_I can't keep them frozen much longer," Elizabeth yells._

"_We're __**not **__leaving you behind."_

_Elizabeth takes a deep breath, trying to concentrate on the machines around her, but John's vow is breaking her concentration._

"_If you don't leave right now, __**none**__ of us will get out of here, so __**go**__," Elizabeth takes a moment to turn slightly to John so he knows she is serious. __**"That's an order."**_

_Suddenly Oberoth is able to gain control and a Replicator fires its weapon at Ronon, barely missing him. He realizes they are fighting a losing battle; he seizes the back of John's TAC vest. "Come on." He grabs at John again, this time giving him a hard yank and John stumbles back a bit._

"_**Elizabeth?" **__John yells, shots fly by both sides of his head, not wanting to give up on her._

_Realizing that she has to be left behind Elizabeth turns to fully face John __**"GO."**_

"I should have thought of something else, had Rodney figure something out. He's always so good under pressure," John thinks to himself. "I should have tied her to the chair before I left, that way she never would've been able to leave the Jumper. I never should have let her go in the first place, I never should have asked." His mind taking him back to another memory.

"_Feel like taking a trip?" John asks as Elizabeth shifts on her bed to face him, Rodney, Ronon and Teyla. _

_She sits patiently, listening to the team talk about how the nanites inside of her could possibly be used against the Replicators._

"_What happens if the Replicators take control of the nanites inside of me?"_

_Rodney looks almost hurt, as if her question is an accusation. "Well, they won't. I would block any attempt…"_

"_But if they do?" Elizabeth asks insistently. _

_John steps up, answering the question with something no one wants to address. "I ordered Rodney to write a kill-switch into the nanites code. If we trigger the program it'll neutralize them."_

_Elizabeth looks down, not wanting to look any of them in the eye. "Neutralize them? You mean shut them off?"_

"_Yes." Comes Rodney's quiet answer._

_Keeping her eyes to the floor, Elizabeth makes the one statement none of them want to talk about, "And you said the nanites are all that are keeping me alive." Lifting her head to face Rodney._

_Her focus turns to John as he answers, knowing he needs to be the one that Elizabeth hears it from. "They are. If we shut them off it will…kill you. But that's not gonna happen all right. I've ordered Rodney to keep an eye on the little bastards, make sure they behave," he says quietly, trying to reassure her._

"_We would not ask this of you if it was not the only chance of this mission succeeding," Teyla says softly and Elizabeth offers a weak smile._

_Rodney gestures to Teyla, "She's right. If we don't get a hold of a ZedP.M. this City and everyone in it are gonna…"_

_Before he can complete the thought Elizabeth looks at John. "When do we leave?"_

_Rodney glances over at John with a look of 'are you sure about this'. To his credit John doesn't flinch a muscle. "Right now."_

_Rodney looks from Elizabeth to John in panic while Ronon leaves to get ready. "What? Wait, no, no, no, no, no, no, no, no, not right now." _

_Teyla nods slightly to Elizabeth, she too leaves the room._

_Rodney looks at John. "Look I haven't finished finalizing the power distri…"_

_John cuts him off. "Finalize it, we need to move."_

_Rodney darts from the room as John steps forward towards Elizabeth. They look at each other intently for a moment before Elizabeth breaks the gaze and looks to the floor._

"_You're gonna be okay Elizabeth." It comes out as a statement; there is no uncertainty in John's voice._

_Elizabeth smiles slightly, wanting to believe her second-in-command with every ounce of her being but knowing better. "Still, I would like all of you to keep a very close eye on me and the first sign of suspicious behavior, do not hesitate with that kill-switch," she says without faltering._

"_Okay, but that's not gonna happen…" John replies, his gaze faltering._

_Elizabeth interrupts John's promise. "John, I mean it," she says with a sternness only reserved for the most serious of decisions._

_John looks up and meets Elizabeth's blazing green eyes, she nods her head infinitesimally; John mirrors the look, nodding in return._

"Power levels are approaching critical. The test only needs another few minutes. Hopefully he's all right," Rodney says, frantically pecking away on his computer.

"Colonel Sheppard can you hear me?" Teyla steps forward toward John but does not touch him. "John? Rodney, are you sure he is in no danger?" Teyla questions, looking from John's almost catatonic state to Rodney's anxious expression.

"For right now? Yes. But if the power levels go above critical we may have to bodily remove him from the Chair," he says looking at Ronon.

"I'm ready, just give me the word," Ronon says, standing closer to the Chair, prepared to yank John out.

For all the talking they're doing about him, John doesn't seem to care; he's too lost in his memories to notice anything else around him.

"_Our people are in the hands of the enemy Doctor. Do you know what that means? It is just a matter of time before the Wraith figure out that this is the base of our operations," John looks at Elizabeth straight in the eye, not backing down an inch._

_Elizabeth stares back needing to get her point across. "I just need more information; I mean who knows maybe we could negotiate a peaceful…"_

_John shakes his head in disbelief. "Peaceful? Are you kidding?" he asks incredulously. "We weren't there for more than a few hours before they showed up," John explains before Elizabeth supplies her explanation._

"_Is it possible they came because of you and that one of these people you brought back here with you tipped them off?"_

"_It's possible," John concedes._

"_See, that is exactly the kind of snap decision I'm referring to."_

"_They're not all bad people and you know if we're gonna stick around here we need friends," John explains, trying to defend his decision._

_Elizabeth takes a deep breath, "Okay I see your point. Now you see mine. I will not authorize a rescue mission unless I am sure there is at least a remote chance of success. I'm not sending more good people, including you to their deaths." _

_John nods, "Okay," he walks away to go back into the Control Room to begin devising a plan._

"How's it looking McKay?" Ronon asks, seeing a small smile flit across John's features.

"Still okay, the levels seem to be holding steady for the moment," Rodney replies while the three friends watch their team leader twitch and fidget.

"It reminds me of when we have overnight missions, when he sleeps. Does that mean he's having nightmares just sitting there?" Ronon muses while Rodney looks at him and then John.

"I have no idea, I have no way of knowing what is going on in his brain and I'm not sure if touching him to attach any kind of medical equipment would be a good thing right now."

"I agree with Rodney, I think we just have to wait and see. We are very limited in options and since he is in no immediate danger, I suggest we let this run its course and see if the Colonel will be able to extract himself from the Chair when he is ready," Teyla says as both Ronon and Rodney look to her to make the right decision.

"What if he's never ready?" Rodney asks the question they are all thinking.

"Ronon is ready to use force like we had originally planned," Teyla says calmly, laying a hand on Rodney's arm.

Meanwhile John's mind is jumping from memory to memory as it focuses on Elizabeth and their time as leaders together. It seems that all it needs is a slight reference point and his memories go from there.

"_Can you believe this?" Elizabeth asks, getting up from the conference table and looking at the picture of the Replicator ships._

"_No…it all seems too good to be true," John answers, while Elizabeth turns startled by her Military Commander._

"_What?"_

"_Well, if those nukes do what Ellis says they do…" John starts to say, swiveling in his chair to face Elizabeth._

"_Since we won back the City we haven't heard so much as a peep from the Replicators."_

"_Well obviously they haven't gone away," John says defending Ellis._

"_No, but maybe they've decided that we are more trouble than we're worth, that the threat of our A.R weapons is enough to keep them at bay," Elizabeth argues trying to convince John._

_John stands and looks right at Elizabeth. "You don't build that many ships to make a run at Atlantis," he says as Elizabeth nods her head in consent. "They're headed for Earth," he continues while both he and Elizabeth stare at the grainy black and white photo on the screen._

_Later, after Elizabeth has tried to talk Ellis out of what he was planning. John goes looking for her after hearing some startling news._

"_Ellis told me that you called Woolsey and General O'Neill and tried to get the whole thing called off," John says, walking up the stairs next to Elizabeth._

"_Yes I did," she answers, not bothering to hide her distaste for the mission._

"_They didn't bite?" John's question comes out sounding more like a statement._

"_They did not," Elizabeth concedes looking over at John._

_Walking toward the catwalk to her office, John gets up the courage to say what's been bothering him all day. "Look, I know you think we're doin the wrong thing here but uh…"_

_Elizabeth stops and looks at him. "John…" They stand there for a heartbeat, seeing that there is no common ground. "Good luck," Elizabeth says, turning and walking away before John can see the pain on her face._

"I let her down that day, there's no other way to say it. She needed me to back her up and I let her down. If I would have backed her like I had a thousand times before she'd be here with us instead of…" John thinks to himself as yet another memory invades his mind.

"_You okay?" John asks, walking over to Ronon's bedside._

"_Yeah I'm fine. They got all the glass out," gesturing to his shoulder. _

"_Good."_

"_You need me somewhere?" Ronon asks wanting to be doing something useful._

"_Right here, getting better."_

"_All right, well I'm good to go."_

_John fiddles with his radio and then he hears. "Colonel?"_

_Taking four steps towards Jennifer and looking over her into the surgery suite as Jennifer puts a hand on his shoulder to lead him to the monitors to the left of the door. John can see someone wrapping Elizabeth's bald head in bandages._

"_Is she okay?" he asks quietly._

"_She's alive but she's in bad shape. She's got six broken ribs, one of which punctured a lung. Amazingly she doesn't have any spinal damage…but her head got knocked around pretty good. She's suffering from a cerebral edema, which may have caused substantial brain damage."_

_John stares at the monitors in horror while his own brain tries to process what Jennifer is telling him. "What does all that mean?"_

_Returning his gaze Jennifer realizes what she needs to tell John. "Well it's too early to know for sure but if she survives…and I gotta stress the __**if."**__ John's eyes leave her and go back to the monitors. "She'll never be the same Elizabeth again."_

_John stares at the screens, letting the news sink in._

"_I'm sorry, I've gotta get some things and get back in there. We're understaffed, most of our team's on the Apollo."_

_All John can muster the strength to do is shake his head in understanding; never taking his eyes off the monitors._

"Oh my God, is he crying?" Rodney asks, looking at John's still form in the Chair. "He is… he's crying."

"What…?"Ronon begins to ask but then realizing he knows the answer.

"Elizabeth," Rodney and Teyla say as Ronon mutters "Dr. Weir." under his breath.

"I think it would be prudent to get him out of there Rodney," Teyla says, seeing the moisture pooling under John's closed eyes.

"I spent three years fighting by her side. I fought against her before but she had never taken it as personally as she had with this fight. Maybe if I fought with her then we wouldn't be fighting without her now," John thinks and suddenly there is a white-hot knife of pain slicing through his body as he feels the City cry out.

Rodney's tablet beeps. "Crap, we need to get him out. NOW," he says abruptly. "We've got alarms going off City-wide. What is going on?"

Before anyone can touch him, John suddenly comes to and sits up. "Rodney…what's going on?" He asks, hearing all the beeping of Rodney's tablet.

"I have no idea. What did you do?"

"I didn't do anything," John says angrily, as suddenly there are blowouts on three of the computers Rodney has set up around the room. "Rodney?" the name comes out as a warning question.

"The Chair is off-line so you might as well go. There's nothing you can do and I need to find out what's going on," Rodney says dismissing John with barely a glance.

"I didn't have anything to do with this. I'm not one of your subordinates, you don't need to talk to me like that," John snipes back, his voice getting louder, his hands close into fists and for a moment Rodney actually thinks he's going to have to defend himself from his best friend. "Let me know when you have whatever is going on figured out," John growls out, turning to leave.

"Go with him, I'll be fine. You won't be any help to me but maybe you can help him," Rodney says defeated, gesturing Ronon and Teyla out of the Chair Room and then tapping his comm. "Zelenka, where are you?"

Ronon and Teyla dash out of the Chair Room after John. They follow him to his quarters. As they near his door it opens without John making a move toward the door controls but then closing before Ronon or Teyla are able to get through.

"Why don't you go and see if you can help McKay? I'll stick with Sheppard and see if I can help him," Ronon suggests to Teyla, exchanging worried glances.

"Radio me if there is anything I can do," Teyla says. Ronon nods in affirmation and Teyla makes her way to Rodney's lab.

Suddenly John's door opens unexpectedly and reveals that he's changed into workout clothes.

Ronon smiles at John as the Military Commander walks rapidly toward the gym. "Great idea, let's go spar and let McKay figure this out."

"Actually Chewy, I was thinking I'd work out on my own if you don't mind. Why don't you go see if there's anything McKay needs help with? I'll be fine, I just need some space," John says, stopping at the doorway of the gym.

"You serious?" Ronon questions, receiving a nod from John. "All right, I don't know how much help I'll be but I'll go. I'm comin' back in an hour to check on you though so no lettin' the dummies get the better of you," Ronon promises, backing away from the door.

"Thanks big guy," John says sincerely as Ronon nods and strides back the way he came.

"_Dr. McKay, I have reports of structural damage coming in from all over the City. Can you please enlighten me as to what is going on?"_ Woolsey's voice can be heard throughout the lab.

"I'd love to but I'm still trying to figure out what's going on as well as shut as many non-essential systems down before the City overloads itself," Rodney says snappishly, striding from one computer to another.

"_Understood, let me know when you have something."_

"You'll be the first, as always," Rodney retorts while the door opens to reveal Ronon alone. "What are you doing here? Where's Sheppard?"

Ronon dumps himself into a nearby chair. "In the gym, he wanted to work out alone."

"Are we sure that's wise?" Teyla asks concerned.

"I told him I'd come back in an hour to check on him. How much damage can he do to himself in an hour?"

Back at the gym, John starts out on the static dummies. Punching and swinging without hand protection at the hard foam, as the memories flood back to him.

"_What's done is done Lieutenant," John says barely looking at Ford, glancing at the young woman in the cell with them._

"_No, first you set off the alarms and then you stop to rescue people when you know damned well the Wraith are on our tail," Ford says angrily watching outside the cell. "It's like you're purposefully sabotaging this mission. You hate to see me succeed at anything," he says, sounding like a five year old._

_John looks from Neera to Ford. "You've got a lot of issues to work out Ford."_

"I...was…supposed…to…take…care…of…him," John says aloud, punctuating each word by hitting the dummy harder and harder.

"_Down that hall fifty meters turn left. It'll take you to Teyla and Ronon's cell," Ford says, looking back down the hall he and John just came from. "I'll hold the Wraith off for ya."_

_John walks back over to Ford. "You're coming with me."_

_He claps John on the arm. "I'll hold the Wraith back boss, now go. I'll be okay," Ford replies._

"_I'm not going without you, Lieutenant," John says softly as Aiden turns around._

"_John, I'll catch up," he pushes John. "Now go," Ford takes off down the hall just as the alarm sounds._

"I was so sure I could bring him home. We're not supposed to leave people behind," John mutters under his breath, staring down at the destroyed dummy laying on the floor at his feet.

"What if it is Sheppard?" Ronon suddenly asks, causing Teyla, Rodney, Radek and a half a dozen other scientists stop and look at him.

Rodney begins tapping on his tablet again. "What are you rambling about?"

"What if it's Sheppard's connection to the City?" Ronon asks again. Rodney looks at Radek who shrugs.

"Do you mean that Colonel Sheppard is causing all of this…chaos?" Teyla asks, looking at Ronon and then turning to Rodney. "How is that possible?"

"What? Like the City is controlling him?" Rodney asks, confused by the talk of something other than a scientific solution.

"You said yourself, he has a connection to the City," Ronon says, standing.

"Yes, to open doors and turn lights on," Rodney pronounces, gesturing with his hands as he always does when he's anxious. "But not to do complex things, like trip alarms and control whole systems," he continues frustrated.

"But Rodney," Zelenka says calmly. "What if Colonel Sheppard's connection to the City is much stronger than even he's aware of?" he asks in a quiet tone.

"We can't worry about the how right now. We need to concentrate on keeping the City from falling apart, however it is happening," Rodney says sensibly and everyone returns to what they were doing.

Back in the gym, John's memories are playing through his mind like movies, one right after another, no order to them whatsoever; it's wherever his mind takes him.

"_This is crazy," John says looking at Teyla._

"_Believe me, this is not a decision I am taking lightly."_

"_But d'you realize what he's asking you to do?" John protests._

"_Doctor Keller assures me that the procedure is completely reversible and will have no lasting ill effects," Teyla tries to reassure her team leader and friend._

"_I'm not talking about the procedure," John says quietly._

"_I know."_

John shakes his head and the memories recede with the realization he has beaten the fourth and last static dummy to pieces. He moves to the punching bag swinging gently in the corner as if beckoning him to fight.

"_So…how long are you planning on keeping me prisoner?" Ronon asks, straining against the restraints holding him to the bed._

_John grimaces, stepping closer. "As long as it takes to clear your head."_

"_My head is clear." _

"_You may be feeling fine right now, but things are gonna get pretty rough for you. We're gonna get you through this."_

"_Whatever you've got planned, it's not gonna work. You've got a choice: you can either kill me or you let me go, and if you let me go I promise I won't come after you or Atlantis."_

As the memory of Ronon writhing in pain fades, another even more painful quickly takes its place.

_Rodney looks at John. "How about we say goodbye now?" He asks quietly._

"_No," John replies strongly._

"_What d'ya mean 'no'?"_

_John looks at Rodney. "I mean I'm not sayin' goodbye."_

"_Well I'm sayin' it anyway," Rodney says, sounding like Rodney._

"_Well I'm not listening."_

_Rodney's shoulders slump inside John's leather field jacket. "Yeah but pretty soon I won't even know who you are." _

"_Then I'll remind you." _

"_Yeah but I don't want you to see me like that. I want you to remember me as I am…as your genius friend not as some…"_

_John nods his head. "Not happening."_

"_Please."_

"_You're stuck with me Rodney, just accept it."_

_Rodney starts to protest. "Yeah, but I…"_

"_No," John says loudly, waving a finger at Rodney. "That's final."_

"I came so close to losing him, way too close," John mutters. The punches he is landing quicken as if his body is trying to rid itself of something.

"_What did you think we were gonna do? Just give you a bunch of Replicator bodies and send you on your way?" John asks looking at the Replicator body housing the consciousness of one of his best friends, leveling his rifle at Koracen and his 9mm at the Fran/Elizabeth Replicator._

"_I truly believed that we were no threat to you," she says genuinely, taking a step toward John._

"_You may think you're Elizabeth, but you're not." _John roars in fury and the bag starts to swing wildly around, not able to bounce back fast enough.

"_It's okay, I'll go first."_ John hears in his head, remembering those last few moments watching that Replicator body with the essence of Elizabeth in it. Those few words took him back to a time when he had seen Elizabeth demand to be one of the first through the Gate on the way to Atlantis. He knew right then that it was Elizabeth.

"No, I knew when she killed Koracen. She was defending me, that's when I knew it was 'Lizabeth," John says, letting out another howl, running from the gym, needing to dissipate the rage any way he can.

Rodney hears a beep on one of the Ancients computers. "Oh God."

"What is it?" Ronon asks, standing suddenly.

"We're starting to have system failures City wide. The City is beginning to overload. It's like it's getting power from a source other than the ZedP.M.," Rodney snaps out, flitting from one computer to the other. "Oh this is not good, not good at all."

"What is it?" Teyla asks looking from Rodney's nervous face to Radek, who slowly turns.

"Fires are breaking out all over the City. Power conduits are shorting out and life support has been malfunctioning, so some areas are filled with pure oxygen…"

"That is helping start the fires," Teyla finishes, with Radek nodding in agreement.

"Oh crap." Comes from the corner where Rodney is tapping away on a computer. "The Halon suppression system is failing."

"How is that possible? I thought after Dr. Weir and Colonel Sheppard were taken over by Phebus and Thalen you were able to make the system less susceptible to attack," Teyla questions, again looking from Rodney to Radek.

"It's not being attacked, it's like…" Rodney starts.

"It's simply failing. If we don't find a way to get the systems regulated it will fail and the Halon gas will be released throughout the City," Radek finishes, as Rodney goes back to pecking on his tablet.

"We need to find Sheppard; he can tell the City to stop what it's doing," Ronon says, starting for the door.

Rodney starts after him. "Like I said, I don't think he's got the ability to talk to the City that way."

"You got a better idea?" Ronon challenges the smaller man.

"No…no I don't." He turns back to Radek, "Keep working from here. If need be we can shut all the systems down, but only as a last resort," Rodney instructs, following Ronon and then Teyla out of his lab.

"_Dr. McKay, please tell me you have some idea of what's going on,"_ comes Richard Woolsey's worried voice over Rodney's comm.

"Yes, the entire system grid that keeps Atlantis running is malfunctioning. There are fires breaking out all over the City. The Halon suppression system is working on putting them out but that system is also showing fluctuations. If it fails completely it could vent Halon gas all over the City," Rodney says rapidly, running after Teyla toward the gym.

"_Can't you just shut the system down?"_

"Not without shutting everything down. I'd have to do a complete override and with the Halon gas that is already being pumped into the City to put out the fires there needs to be a ventilation system on to pump the gas back away from the inhabitants. If I turn that off, the gas would be trapped in the City and would settle into populated areas."

"So what do we do?" Woolsey asks, pacing in front of Chuck's console in the Control Room.

"We're going to attempt to talk to the City, to see if we can get it to bring the systems back on-line," Rodney says, realizing how crazy that sounds, even to him.

"Excuse me? Did you just say you were going to _talk _to the City?" Woolsey asks while Chuck raises an eyebrow at Amelia.

"Yes, that's what I said."

"_And how are you going to do that?"_

"We're going to use Colonel Sheppard," Rodney says in that innocent convincing tone he uses only when trying to convince John of some harebrained scheme, like bringing an Ancient power source and weapon back on-line.

"_And how is he going to help you?"_ Woolsey questions, trying to understand what Rodney is proposing to do.

"I don't know just yet. I'll let you know if it works," Rodney says, quickly tapping off his comm as the three teammates get to the gym.

When the doors open they all try to grasp what they are seeing.

"Oh poor B.O.B.," Rodney says quietly, seeing the urethane foam filler of the static dummies laying everywhere.

Teyla bends over to pick up pieces of broken bantos sticks that litter the floor. "What happened in here?"

"Someone got a workout, that's for sure," Ronon says. Looking the room over, his gaze falls to the punching bag that usually hangs by two chains; it is now dangling from one.

"Well, at least he got his frustration out," Rodney comments following Ronon's gaze seeing the bag's shiny appearance. "Looks like he worked up a sweat."

Having a different idea of what is on the bag, Ronon strides over and wiping a hand down the bag, turning to Rodney, flipping his hand over.

Rodney's eyes widen to the size of dinner plates as he questions, "Is that…?"

"Blood," Ronon answers him.

"My God, what is he doing to himself?" Rodney asks, looking at Ronon and Teyla.

"Trying to make the pain go away," Ronon says simply. "Any way he can."

"We've got to stop him. Where would he have gone from here?" Rodney asks looking around the room for clues as Teyla moves away and taps her comm.

Ronon points to the floor at the blood droplets leading back out the door. "Why not follow the blood?"

"The Colonel is not responding to my repeated attempts to communicate. Either he is unwilling to talk or taken his headset off," Teyla informs McKay and Ronon. They follow the slight trail of drops down the corridor.

"They're leading to his quarters. We need to move," Ronon states, realizing the direction they are moving in.

"_Rodney, can you hear me?"_ Radek inquires in Rodney's ear.

"Yeah Radek, can it wait?" Rodney asks sharply.

"_Not really. The suppressant system is going critical; it will fail any minute."_

Meanwhile, John is in his quarters, ravaging his belongings while his memories are ravaging his mind.

"_You can quit now, I'm not afraid of you," John says, facing himself._

"_Oh yes you are, I'm the one thing you are afraid of. You failed your friends, you brought this on them and there is __**nothing**__ you can do to stop it," the alien John states matter-of-factly and John feels the anger welling up inside him._

The destruction is immense for such a small area. In no time John has ripped his Johnny Cash poster off the wall and into shreds. Overturned his bed, ripping the sheets when he flipped the mattress. Swept everything off his desk, including his laptop, which clatters to the floor in at least a few pieces. He grabs his copy of War and Peace and throwing it across the room where it hits the wall with its spine, breaking the book into several sections and the pages flutter to the floor.

"You're the reason Heightmeyer's dead," John says, throwing some of his model airplanes around the room. "You killed Sumner," the voice gets louder as suddenly more books are flying across the room.

"John, can you hear me? You need to open the door. We need to talk to you, it is urgent," Teyla pleads from where she stands with Ronon and Rodney outside.

"Sheppard, come on, open up," Ronon demands, banging on the metal door.

"He either can't hear us or doesn't want to hear us," Rodney says shouldering up to the door. "I'm gonna have to try to override the lock. Radek, how do things look on your end?" Rodney says pulling the front off the oblong panel, tapping his comm.

"System is still critical, there is no telling how much time you have," the Czech replies pushing up his glasses.

"Nothing like a little pressure," Rodney mutters under his breath, jumping visibly as there is a loud thunk against the door. "What the hell was that?"

"I'm guessing the Colonel is getting quite physical with his belongings," Teyla says after they hear another thud.

"You're the reason Ford is still missing," John shouts throwing his guitar against the wall where it shatters against the metal wall. He picks up his golf bag and heaves it across the room-clubs tumble out and scatter around the floor and some of the heads shatter on impact. Picking up the Athosian pot, John begins to heave it without much thought as to what he has in his hand. "You're the reason Elizabeth is floating out in the vacuum of…" he shouts hoarsely. As the pot comes into his line of sight, John realizes what he is about to do and it stops him dead in mid-throw.

"John…John can you hear me?" Teyla asks urgently when the trio notices the muffled shouting and random thuds have stopped.

"Sheppard, open the door. You need to let us in. We need to help you," Rodney says. The door suddenly slides open and John is revealed to his team.

"Sheppard, are you okay?" Ronon asks while he, Rodney and Teyla carefully make their way into his quarters.

When John doesn't respond Teyla moves a little closer. "John, can you hear me?" she asks, seeing John's eyes aren't focused on her but some unseen point beyond her.

"What the hell did he do in here?" Rodney looks around the room at the debris littered on the floor.

_"Rodney? McKay can you hear me?"_ Radek's voice comes over the comm.

"Yeah Radek, now what's wrong?" Rodney sighs, not knowing how much more bad news he can take.

"Nothing, the systems have all gone back to normal. The fires are mostly out and the Halon suppression system is back in the green. Aside from minor structural damage, Atlantis is going to be fine," Radek relays, looking at his computer as Rodney flips his tablet over and begins pecking away.

"He's right. All the systems are out of critical and back to normal functions. We're gonna be okay." Rodney chuckles nervously looking up to Teyla and Ronon.

"Not all of us," Teyla responds, turning to John. "John, can you hear me?" This time she takes a step closer and puts a hand on his arm. She realizes he is holding something in his right hand. "That is a hand-made Athosian pot. Very rare and very priceless by my people's standards. It is one of a kind," she says softly, recognizing the work.

"I gave it to Elizabeth for her first birthday here," John says in a monotone, the hoarse voice getting Ronon and Rodney's attention.

"What a very wonderful and thoughtful thing to do for a friend. I remember this sitting on Elizabeth's desk where she could always see it. It must have meant a great deal to her."

"I took it from her desk after…after her accident. I didn't want to risk it getting sent back with all her other things; it belongs here."

"She would agree with you. Why don't you let me take it? I'll put it right over here." Teyla gently takes the pot from John's reluctant hands and places it carefully on the long dresser next to his overturned bed, where he can still see it.

"Sheppard," Ronon calls out, stepping toward the older man as John falters and hits the floor on his knees.

"I told her once that she'd be okay. It was the only way I could think of to promise her that I'd always be there to look out for her and keep her safe." John chuckles sardonically. "I spent the next two years giving her sleepless nights and more stress than any one person should ever have to handle and on top of that I failed not once, not twice but three times to keep the promise I made her," John murmurs looking over to the pot. "That A.I. was right. If I can fail the one person who gave me her faith and trust so blindingly and unconditionally, how can I protect anyone else in this City?"

Suddenly there is a sharp crack in the room as skin strikes skin. "If Elizabeth were here she'd have done the same thing," Teyla says calmly as Rodney and Ronon see her lower her hand. "You are not a failure, John Sheppard. Elizabeth chose to stay behind when the Replicators attacked; she did that of her own free will to protect all of us and this City."

"But if I had stood by her when Ellis first came to us, maybe she'd still be here," John poses the statement as a question, looking up at Teyla.

Rodney takes a step closer to his friend. "How could you have known what would happen? What are you Superman?"

"No, Mr. Fantastic," John whispers with a trace of sarcasm.

"Ronon, please help me get John's bed straightened so he can sit down?" Teyla asks. She and the Satedan move away from John as Rodney moves closer.

"I'm the one who reactivated Elizabeth's nanites. I'm the one who made her the perfect tool to use against the Replicators," Rodney states squatting down to look John in the eye. "You were against that from the beginning. You knew she didn't want that kind of existence. I didn't listen to you and…I should have," Rodney bows his head in shame.

"But you were right; going after the Replicators when we clearly weren't ready was like poking a sleeping dragon, we shouldn't have done it, I should have stood by you and Elizabeth," John says, searching for Rodney's eyes to make contact.

"John, why don't you come over here and sit down." Teyla puts a hand under his left arm and Rodney straightens up and grabs his right to help him stand. "John! Your hands," she gasps as she, Rodney and Ronon finally see the bloody mess he's made of his hands.

"We need to get you to the Infirmary, Jennifer needs to look at your hands," Rodney pleads, as John vehemently shakes his head.

"I'm fine. I can still move my fingers so I know they're not broken. They're just a little cut up."

"Are you out of your mind? Do you know the infections you could get?"

John looks as Rodney. "I'm fine Rodney; I don't want everyone in the City to know their Military Commander went bonkers and tore up his hands."

"Might I suggest Jennifer come here with a few medical supplies to assess the damage to your hands and to also check on your other injuries that you have no doubt aggravated?" Teyla asks, looking at John hopefully.

"All right," John compromises, knowing his teammates won't leave him alone otherwise.

While Teyla turns to call Jennifer, Rodney steps forward carefully. "I should probably let Woolsey know everything's fine that the City isn't gonna sink into the ocean after all. I'll keep what I tell him to a minimum, he doesn't need…"

"Rodney, tell him. He needs to know and we need to figure out what was going on," John interrupts, gazing at his friend.

Rodney nods and taps his comm. "Mr. Woolsey, I thought you'd like to know that all the systems are back on line and out of critical mode. The Halon is strictly putting out the few remaining fires but the system as a whole is working properly," Rodney says, attempting cheerfulness.

"Sensors are giving us reports now. It seems whatever you've done has once again saved the City and its inhabitants," Woolsey says, looking over Chuck and Amelia's shoulders.

"Yes about that…" Rodney replies, looking at Teyla and Ronon nervously.

"_Why don't we debrief in the morning? It's been a long day for all of us and I'm sure you could use some rest,"_ Woolsey remarks as John smiles.

"Well we were gonna go to the mainland tomorrow…" Rodney begins to say.

"We'll be there 0700 sharp," John says over Rodney and Woolsey's head snaps up at his second-in-command's voice.

"_Very good Colonel Sheppard, 0700 it is."_

"But…but the mainland...?"

"Can wait Rodney. It'll still be there when we're done with Woolsey," John says, exasperated.

"Okay, where's my patient? Good God what happened in here?" Jennifer asks, walking into John's quarters and seeing the mess.

"Rearranging and spring cleaning," John says sheepishly while Jennifer kneels at his feet, setting her kit next to her.

"Except it's technically almost winter Colonel," Jennifer responds, pulling on a pair of gloves.

"I'll be back," Ronon says simply with a nod to Teyla.

"Rodney, why don't we get some boxes and begin cleaning up in here?" Teyla questions encouragingly.

Rodney looks around the room. "Yeah, sure. I'll get some boxes from my lab to put stuff in."

"Leave my planes. I can fix those; I just need a little glue," John says through his teeth as the sting of the antiseptic begins.

"I'll get new sheets, a blanket and pillows for your bed," Teyla says, smiling at John.

"And I'll get the glue. I've got some really great industrial stuff that'll have your planes looking like new in no time," Rodney adds, following Teyla so Jennifer can examine John in private.

"You'll be fine. You haven't broken any bones in your hands. There are just cuts and scratches. Your back _was _on its way to healing but you've stretched the skin around some of the more severe burns. It'll take a day or two, but you'll be fine," Jennifer says after twenty minutes of bandaging.

"Thanks Doc." John smiles at the young woman.

"Get some rest. I'll leave you some more sleeping pills." She puts a hand up when John opens his mouth. "I know you don't like taking them, I'm not saying you _have_ to. I'm just saying they're here in case you need them." She smiles, setting three blister packs on the dresser next to Elizabeth's pot.

"Thanks," John says as Jennifer smiles and leaves just as Ronon walks back in.

"Gym's clean," he says simply.

"Thanks big guy, I appreciate it. I completely forgot about that. How bad was it?" John inquires, rubbing his forehead and looking up at Ronon.

"You'll need to requisition more static dummies and we'll need to get a whole new supply of bantos sticks, but other than that, not bad," Ronon answers with a chuckle.

"Great. Woolsey's gonna have a heart attack. Those B.O.B.s aren't cheap."

"The bantos sticks won't be hard to replace, I can help with that. We'll have plenty in no time."

"Thanks."

"Teyla was right to cuff you, ya know."

"What?" John asks, thinking he hadn't heard Ronon right.

Ronon crosses the room, leaning on the dresser next to Elizabeth's pot, looking down at it. "She wouldn't blame you and she'd be pretty pissed that you tried to bring the City down. She sacrificed herself for this place and for all of us so we could go on."

"But we shouldn't be going on without her," John says quietly staring down at his bandaged hands. "Oww, what was that for?" he yelps, feeling Ronon slap him in the back of the head.

"You do it to McKay when he does something stupid or complains about something he can't change," the Satedan remarks simply.

"Yeah but…" John begins to say, but then he looks up at Ronon's crossed arms and impassive face. "Yeah."

"Here we are. We've got sheets, blankets, pillows, glue and boxes," Rodney pronounces, struggling in after Teyla and almost tripping over the load in his arms.

John slowly stands to face his teammates… his family. "Thanks guys, I can't tell you how much I appreciate this."

"Do you need any help making the bed or cleaning up?" Teyla asks, gesturing at John's bandaged hands.

John follows her gaze and flexes his fingers. "No, I should be fine if I take it easy. I'll be all right," he reassures them. "I think I'd just like a little time alone to clean up."

Rodney opens his mouth to object but John stops him. "I'll call if I need anything, I promise. You've all gotta have better things to do than baby-sit me. Really, I'm okay."

"I probably should go to my lab and make sure that everything's okay there," Rodney says, walking to the door.

"And I'll go see if anyone needs help with the fires or cleanup," Ronon says as John lightly claps him on the back.

"There ya go."

"And I should check on Torren. You will call if you need us?" Teyla says, already following Rodney and Ronon to the door.

"I promise. I'll see you all in the morning, 0700 and yes Rodney, I'll set my alarm," John answers Rodney's unsaid question.

Once alone John turns to survey his room. "It's gonna be a long night," he muses, picking up some pieces and putting them into the container Rodney brought back with him.

The next morning dawns bright and clear. A perfect day to go to look for potential campsites on the mainland.

Never having made it to bed, John is ready before everyone else. After checking in at the Infirmary, he heads down to the mess to get a cup of coffee, deciding to go out to the balcony off the Control Room to watch the sunrise and ready himself for the meeting with Woolsey and his team.

"Wow," he says softly. The sunrise mixes a flourish of pinks and purples with the blue of the fading night. "It might not be where we started 'Lizabeth, but this is still one hell of a view," he says softly, sipping his coffee, remembering the countless sunrises and sunsets he has seen off this balcony.

"_There you are." John walks out onto the balcony, carrying his pack._

"_Hey, I was just stealing a breath of fresh air," Elizabeth says, uncrossing her arms and leaning over the railing. "I thought you were off exploring the City," she turns away to look out over the water._

_John reaches into his pack. "About to," he replies, pulling out a bundle of cloth. "Picked this up on the mainland; the Athosians made it." He holds it out to Elizabeth and she takes it, gently cradling it in her hands. "Happy birthday," he says seriously, looking Elizabeth in the eye with just a glint of a smile._

_Elizabeth eyes him, but remembering her manners, smiles and unwrapping cloth. "Mmm," she murmurs, trying to see what it is. When she gets it unwrapped she tilts it back to study the craftsmanship. "It's beautiful," she says honestly. "How'd you find out?" she asks, looking up at John, trying not to smile._

_John shrugs. "Mum's the word," raising his eyebrows in mischief, leaving Elizabeth with her gift._

John chuckles at the memory of the look on Elizabeth's face, then his comm beeps. _"Colonel Sheppard, do you have a moment?"_ Woolsey asks.

"Sure, I'm out on the balcony off the Control Room. It's a beautiful morning, care to join me?" he asks, hearing the door sliding open behind him.

"It _is_ a beautiful morning. Wow, that is incredible," Woolsey murmurs when he sees the sun shining brightly. He turns to John and gets to the point. "I wanted to let you know that I've asked Dr. Kwiatkowski to sit in on the debrief. I think she might have some unique views on what has happened and hopefully a way to make sure it doesn't happen again," he says.

"Okay," John says with a noncommittal shrug of his shoulders, knowing Woolsey won't be swayed.

"Well, everyone should be along shortly, so whenever you're ready," Woolsey says, starting to walk away and then turning back. "I'm very glad you weren't seriously injured. It would be a great detriment to this expedition and this City if something were to happen to you."

"Thanks Mr. Woolsey. I'll be a minute," John says over his shoulder, not able to look at the expedition leader.

Turning to take one last look over the water John's attention is caught by a crack in the girder he is leaning next to. Knowing that it happened the day before-that he was responsible for the fracture-squeezes John's heart painfully. "I know how you feel," he murmurs, holding his bandaged hand up to the girder. "I'm so sorry, I would never want to see any harm come to you. I've sworn to protect you with my last dying breath and that's what I intend to do," John promises, taking his hand away. Astoundingly the girder is whole, the fracture gone.

"_Hey Sheppard, where are you? You're gonna miss my presentation,"_ Rodney questions in John's comm and John chuckles a little.

"I'm coming Rodney, hold your horses," he says, smiling at the view one more time and heading inside.

"Oh, there you are. How are you this morning?" Rodney asks anxiously.

"I'm fine Rodney. A little sore but other than that, I'm okay."

"Did you get any rest?" Teyla asks, concerned for her friend.

"Some. It took most of the night to clean up. It was kind of slow going," John says, holding up his hands.

"Have we figured out what was going on?" Woolsey asks from where he sits on the edge of his desk.

"From what I can surmise, I think the City was communicating with Colonel Sheppard," Rodney says as Teyla and Ronon both look up at him. "Yes…well, I go the idea from Teyla and Ronon," he says quietly, bowing his head a little.

"Can you describe what it felt like?" Woolsey looks to John for answers.

"There were times when I was lost so deeply in memories that I had no idea of what was going on around me," John admits thoughtfully.

Ronon leans forward. "Like the other morning, when we were sparring?"

"Or yesterday in the Chair? We kept trying to get your attention and it was like you were off in la-la land," Rodney says as Teyla nods.

"But what about the power spikes?" Woolsey asks, crossing his arms. "Are those going to happen again?"

"From the time stamps and from what the Colonel could tell me, it was the intensity of his memories that were causing the spikes," Rodney comments, trying to relay information.

"Colonel Sheppard was poisoning the City," Riley says simply, walking in. "I'm sorry I'm late, I had an emergency."

"I'm sure," Rodney says somewhat snidely.

"Rodney," John mutters warningly under his breath.

"I know you don't have any faith in anyone in my profession Dr. McKay, but I've had some time to go over all the information that I was given and from having observed Colonel Sheppard the other day-even for a short time-that is the best and most understandable way to put it."

"How do you mean, poisoning the City?" Woolsey asks, leaning forward.

"The Colonel and the City are connected through the ATA gene the Colonel possesses. Therefore, everything the Colonel feels the City will feel."

"So why doesn't Sheppard feel things from the City, huh?" Rodney asks as Ronon cuffs him in the back of the head. "Oww."

"Thanks big guy. Rodney, knock it off," John says forcefully.

"Actually Colonel, it's a viable question. I believe it is because the City can control itself, which is not to say you can't. I just think in this particular instance your encounter on the mainland with the Sakari A.I. weakened you somewhat and the City sensed that and wanted to help," Riley explains.

Woolsey's forehead creases in thought. "Wanted to help?" he asks

"I think the City sees Colonel Sheppard as its favored son, if you will. Since your gene is the strongest in the City, it recognizes you as an Ancient or as close as it can versus someone like Major Lorne, Dr. Beckett or Dr. McKay."

"So you're sayin' that the City sensed Sheppard in pain and it tried to help? How?" Ronon asks wanting to grasp what everyone is saying.

"By trying to sap away the negative emotions, the rage, sorrow, pain, frustration. It was trying to bleed those emotions away from you but it ended up overloading itself and the only way it knew to warn anyone was to trigger the alarms, any of them. I think the City was trying to get your attention Dr. McKay," Riley says, turning to Rodney.

"Of course, when in doubt turn to the…"

"The City knows you and Colonel Sheppard are teammates, friends even. It thought that you would know what to do to help him."

"Are you saying the City is aware of us? That it is a sentient being?" Woolsey sputters.

"It's always been aware of the ones possessing the ATA gene, Mr. Woolsey. I'd venture a guess that it feels a close connection to Colonel Sheppard and anyone he, in turn, is close to. It was essentially trying to get Dr. McKay's attention so he would help the Colonel in ways it can't."

Teyla leans closer. "Since it can't verbally communicate, it did the only thing it could and that was the power spikes and alarms. Knowing, or at least hoping, that Rodney would put the two together."

"Boy was She barkin' up the wrong tree," John mutters sarcastically under his breath.

"I can hear you, you know."

John smiles good-naturedly at his friend's sour expression. "I know Rodney, I know."

"So, where do we go from here?" Woolsey asks worriedly. "Will this happen again?"

"I don't know; all I can do is make guesses. I've never seen anything like this nor tried to counsel someone through something like this," Riley says honestly, shrugging her shoulders. "Until now you've managed to do a remarkable job with keeping your emotions in check. I honestly think the episode with the Sakari A.I. is the start of all this and only time is going to help. But this does prove its point, you torture yourself every day Colonel, and these past few days were visible proof of that."

John looks to everyone in the room and grimaces; knowing everyone was very worried about him. "Sorry about that."

"One thing I would like to recommend is that we begin studying the connection between the ATA gene carriers and the City, _carefully_. This is not something to be done blindly or hurriedly. I think it would be a good idea to get to know the City on a sentient level, if that is at all possible, if it will even let us," Riley remarks, turning to Woolsey.

"Agreed. I think this is a new dimension of the City and it is not one to be trifled with or taken lightly. Use whatever resources you think would be helpful and we'll go from there," Woolsey says. "If I'm not mistaken you have a reconnaissance mission of great importance Colonel, and I don't want to take up any more of your time," Woolsey concludes while the team stands.

Riley speaks quietly. "Actually, if I could have a moment with Colonel Sheppard in private?"

"Sure, I'll meet you guys in the Jumper bay," John says, smiling at his teammates.

"Of course Colonel. Take all the time you need," Teyla says, nodding to Riley as she and Ronon herd Rodney out of the room and Woolsey follows.

"I don't want to keep you; I would just like to know how you feel? Not physically, I can see you have some mending to do," Riley motions to John's hands. "I was wondering about emotionally?"

"Honestly? Okay. Drained but okay. It was all so vivid; every memory was like a movie in my head."

"I think that was the City's influence on you. I'm assuming that it was taking your emotions and amplifying them to a degree that it felt like you were living the experiences all over again."

"It sure felt that way," John says, rubbing the back of his neck, mindful of his bandages. "So I guess this means I'm gonna have to learn the way to your office after all," he says shifting his weight, getting uncomfortable.

"Why? Did you want to?" Riley asks with a twinkle in her hazel-green eyes.

"Ummm, I guess I thought I'd be having to set up regular appointments," John explains, confused.

"Not unless you want to. Like I said the other day I don't think you need your head shrunk, but my door is always open _if _you want to talk. Personally, I think you'd do better talking to your family. Let them in more, they just want to help." Riley turns and begins walking out to the catwalk with John falling in step with her. "Dr. McKay on the other hand, I would have a field day with him."

"I don't know Doc, McKay's mind is a scary place. It's not for the faint of heart," John jokes back.

"Thanks for the tip. Have a safe and illuminating trip Colonel," Riley chuckles as John returns the smile. Nodding to Woolsey, he walks through the Control Room and down the stairs seeing Rodney, Ronon and Teyla waiting for him off to the side of the Gate.

As John gets to the bottom of the stairs and ambles toward his team, his eyes-as well as the others-automatically wander up to the empty balcony where Elizabeth always stood to see them off and welcome them back home. "I don't think I'll ever get used to that," he whispers quietly, not realizing that Riley can see them and hear him.

Both Riley and Woolsey smile, hearing Rodney asking John's advice on asking women out. Something about a presentation he has been invited to back on Earth and wanting to ask someone to go with him.

They stand together on the catwalk, looking at the massive Gate. "I'd like to thank you Doctor, for all your help with this. I look forward to your recommendations on how to communicate with the City and possibly be able to establish a better, more productive relationship with it."

"All part of the job Mr. Woolsey. I would like to make one more recommendation to you professionally on behalf of Colonel Sheppard, his team and the City at large."

"Of course. Whatever you think is necessary, I'll try to make it happen," Woolsey readily agrees; wanting to help the people he is growing attached to.

"Exhaust every resource you have at your disposal to bring Dr. Weir home," Riley states before turning and leaving the expedition leader speechless.

Thank you to those who stuck with the story, feel free to review. I'd love to know what you think!!


End file.
